Worldwide Protein Data Bank
Names
More detailed information about this field from each metasource.
Worldwide Protein Data Bank
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
wwPDB
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
PDB
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank (PDB)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
pdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
Protein Data Bank
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Names
More detailed information about this field from each metasource.
Worldwide Protein Data Bank
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
wwPDB
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
PDB
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank (PDB)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
pdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
Protein Data Bank
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
Other names: wwPDB, PDB, The Protein Data Bank (PDB), pdb, Protein Data Bank
Names
More detailed information about this field from each metasource.
Worldwide Protein Data Bank
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
wwPDB
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
PDB
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank (PDB)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
pdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
Protein Data Bank
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA).
Description
More detailed information about this field from each metasource.
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA).
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The wwPDB is composed of the RCSB PDB, PDBe, PDBj and BMRB.
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
Global repository for all bona fide protein structure data. Single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. It also has RESTful interface to search and retrieve data from the Protein Data Bank (PDB).
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
Webpage:
https://www.wwpdb.org/Webpage
More detailed information about this field from each metasource.
https://www.wwpdb.org/
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://www.wwpdb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://www.wwpdb.org/
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
http://www.pdb.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
Licence:
Name: PBD - specific, files are free of all copyright restriction (including commercial use). Attribution required.Licence name
More detailed information about this field from each metasource.
PBD - specific, files are free of all copyright restriction (including commercial use). Attribution required.
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
wwPDB Privacy and Data Usage
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
http://www.wwpdb.org/about/privacy
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://www.wwpdb.org/about/agreement
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
Publications:
(22)
Publications
More detailed information about this field from each metasource.
Announcing the worldwide Protein Data Bank
PMID: 14634627
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
PMID: 17142228
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Protein Data Bank: the single global archive for 3D macromolecular structure data
PMID: 30357364
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Validation of Structures in the Protein Data Bank
PMID: 29174494
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
PMID: 28190782
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
PMID: 25540181
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank archive as an open data resource
PMID: 25062767
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank at 40: reflecting on the past to prepare for the future
PMID: 22404998
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The future of the Protein Data Bank
PMID: 23023942
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
PMID: 29688351
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
PMID: 30988261
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The archiving and dissemination of biological structure data
PMID: 27450113
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
How community has shaped the Protein Data Bank
PMID: 24010707
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Safeguarding the integrity of protein archive
PMID: 20110969
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1038/nsb1203-980
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
http://dx.doi.org/10.1038%2Fnbt0807-845
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://doi.org/10.1007/s12033-008-9127-7
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1038%2F543179a
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1101%2F110825
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1007%2F978-1-4939-7000-1
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1107%2F97809553602060000896
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1093/nar/28.1.235
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
Publications
More detailed information about this field from each metasource.
Announcing the worldwide Protein Data Bank
PMID: 14634627
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
PMID: 17142228
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Protein Data Bank: the single global archive for 3D macromolecular structure data
PMID: 30357364
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Validation of Structures in the Protein Data Bank
PMID: 29174494
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
PMID: 28190782
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
PMID: 25540181
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank archive as an open data resource
PMID: 25062767
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Protein Data Bank at 40: reflecting on the past to prepare for the future
PMID: 22404998
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The future of the Protein Data Bank
PMID: 23023942
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
PMID: 29688351
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
PMID: 30988261
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The archiving and dissemination of biological structure data
PMID: 27450113
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
How community has shaped the Protein Data Bank
PMID: 24010707
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Safeguarding the integrity of protein archive
PMID: 20110969
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1038/nsb1203-980
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
http://dx.doi.org/10.1038%2Fnbt0807-845
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://doi.org/10.1007/s12033-008-9127-7
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1038%2F543179a
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1101%2F110825
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1007%2F978-1-4939-7000-1
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1107%2F97809553602060000896
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://dx.doi.org/10.1093/nar/28.1.235
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
-
Announcing the worldwide Protein Data Bank
PubMed citations: 899.
899 articles citing: Announcing the worldwide Protein Data Bank
Fusion protein strategies for cryo-EM study of G protein-coupled receptors. PMID:35902590
Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure. PMID:35899067
Combining empirical knowledge, in silico molecular docking and ADMET profiling to identify therapeutic phytochemicals from Brucea antidysentrica for acute myeloid leukemia. PMID:35895695
Naturally Occurring 8ß,13ß-kaur-15-en-17-al and Anti-Malarial Activity from Podocarpus polystachyus Leaves. PMID:35890200
Palladium(II) Complexes of Substituted Salicylaldehydes: Synthesis, Characterization and Investigation of Their Biological Profile. PMID:35890184
Differences in Charge Distribution in Leishmania tarentolae Leishmanolysin Result in a Reduced Enzymatic Activity. PMID:35887004
Data Size and Quality Matter: Generating Physically-Realistic Distance Maps of Protein Tertiary Structures. PMID:35883464
Design, Synthesis, and Anti-Inflammatory Activity of Some Coumarin Schiff Base Derivatives: In silico and in vitro Study. PMID:35860526
Selective activation of Gαob by an adenosine A1 receptor agonist elicits analgesia without cardiorespiratory depression. PMID:35851064
Conserved recombination patterns across coronavirus subgenera. PMID:35814334
Discovery of Phenylcarbamoylazinane-1,2,4-Triazole Amides Derivatives as the Potential Inhibitors of Aldo-Keto Reductases (AKR1B1 & AKRB10): Potential Lead Molecules for Treatment of Colon Cancer. PMID:35807227
Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure. PMID:35794153
Identifying molecular structural features by pattern recognition methods. PMID:35765452
Structural basis of Omicron immune evasion: A comparative computational study. PMID:35763933
In Vitro, In Vivo and In Silico Characterization of a Novel Kappa-Opioid Receptor Antagonist. PMID:35745598
4-Chlorophenyl-N-furfuryl-1,2,4-triazole Methylacetamides as Significant 15-Lipoxygenase Inhibitors: an Efficient Approach for Finding Lead Anti-inflammatory Compounds. PMID:35721976
Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. PMID:35709986
Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble. PMID:35705565
Adamantane-Monoterpenoid Conjugates Linked via Heterocyclic Linkers Enhance the Cytotoxic Effect of Topotecan. PMID:35684313
Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. PMID:35679182
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV. PMID:35664235
Structural Features of Clostridium botulinum Neurotoxin Subtype A2 Cell Binding Domain. PMID:35622602
Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus. PMID:35604094
Structural characterization of a cross-protective natural chimera of factor H binding protein from meningococcal serogroup B strain NL096. PMID:35601959
The Magic of Linking Rings: Discovery of a Unique Photoinduced Fluorescent Protein Crosslink. PMID:35574633
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. PMID:35539058
Validation analysis of EMDB entries. PMID:35503203
Applying polypharmacology approach for drug repurposing for SARS-CoV2. PMID:35498548
Three-dimensional structure determination of protein complexes using matrix-landing mass spectrometry. PMID:35478194
Immunoinformatics approach of epitope prediction for SARS-CoV-2. PMID:35441904
Mining anion-aromatic interactions in the Protein Data Bank. PMID:35440982
Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase. PMID:35425333
Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor. PMID:35425186
In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. PMID:35423962
The inhibition of Mpro, the primary protease of COVID-19, by Poria cocos and its active compounds: a network pharmacology and molecular docking study. PMID:35423770
Are transient protein-protein interactions more dispensable? PMID:35404956
Protein-conjugated microbubbles for the selective targeting of S. aureus biofilms. PMID:35340817
Design of protein-binding proteins from the target structure alone. PMID:35332283
NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. PMID:35328522
The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane. PMID:35300425
Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins. PMID:35288548
Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens. PMID:35195438
Hydrogen Bonds with Fluorine in Ligand-Protein Complexes-the PDB Analysis and Energy Calculations. PMID:35164270
Mechanistic Characterization of the Pharmacological Profile of HS-731, a Peripherally Acting Opioid Analgesic, at the µ-, δ-, κ-Opioid and Nociceptin Receptors. PMID:35164182
Allosteric control of Ubp6 and the proteasome via a bidirectional switch. PMID:35149681
Integration of software tools for integrative modeling of biomolecular systems. PMID:35149213
Prediction the Molecular Mechanism of Shengmai Injection in Acute Treatment of COVID-19 Based on Network Pharmacology. PMID:35136386
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Highly Antiproliferative Latonduine and Indolo[2,3-c]quinoline Derivatives: Complex Formation with Copper(II) Markedly Changes the Kinase Inhibitory Profile. PMID:35104137
SAXS Reveals the Stabilization Effects of Modified Sugars on Model Proteins. PMID:35054516
Molecular docking-based computational platform for high-throughput virtual screening. PMID:35039800
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Group depositions to the Protein Data Bank need adequate presentation and different archiving protocol. PMID:35000237
The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina. PMID:34981769
Computational Approaches for Supporting Combination Therapy in the Post-Aducanumab Era in Alzheimer's Disease. PMID:34966890
Potential role of embelin in the prevention of Freund's adjuvant induced inflammation and ROS. PMID:34966633
Vitamin D3 Prevents the Deleterious Effects of Testicular Torsion on Testis by Targeting miRNA-145 and ADAM17: In Silico and In Vivo Study. PMID:34959623
Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. PMID:34923703
COVID-19: Invasion, pathogenesis and possible cure - A review. PMID:34919978
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
DE-STRESS: a user-friendly web application for the evaluation of protein designs. PMID:34908138
Ten things I `hate' about refinement. PMID:34866607
New system for archiving integrative structures. PMID:34866606
Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2. PMID:34850606
Spectroscopic/Computational Characterization and the X-ray Structure of the Adduct of the VIVO-Picolinato Complex with RNase A. PMID:34847328
Mapping the electrostatic potential of the nucleosome acidic patch. PMID:34837025
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. PMID:34819324
Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. PMID:34804544
Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca. PMID:34789753
A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure. PMID:34762696
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. PMID:34733103
Improving sampling of crystallographic disorder in ensemble refinement. PMID:34726164
Network Pharmacology-Based Analysis on the Action Mechanism of Oleanolic Acid to Alleviate Osteoporosis. PMID:34723038
A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19. PMID:34718395
Dispatched uses Na+ flux to power release of lipid-modified Hedgehog. PMID:34707294
Rational design of chimeric Multiepitope Based Vaccine (MEBV) against human T-cell lymphotropic virus type 1: An integrated vaccine informatics and molecular docking based approach. PMID:34705829
GRP78: A possible relationship of COVID-19 and the mucormycosis; in silico perspective. PMID:34695683
Implementation of Vaccinomics and In-Silico Approaches to Construct Multimeric Based Vaccine Against Ovarian Cancer. PMID:34690620
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
AI revolutions in biology: The joys and perils of AlphaFold. PMID:34668287
Data reduction for serial crystallography using a robust peak finder. PMID:34667447
Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies. PMID:34663870
Match_Motif: A rapid computational tool to assist in protein-protein interaction design. PMID:34648221
Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations. PMID:34639036
Binding Characteristic of Various Antibody Formats Against Aflatoxins. PMID:34632185
Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. PMID:34631338
Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. PMID:34611862
Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis. PMID:34605436
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation. PMID:34580601
Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. PMID:34577164
A method for intuitively extracting macromolecular dynamics from structural disorder. PMID:34535675
Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150. PMID:34535641
Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. PMID:34506130
Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. PMID:34502559
Chemical Composition and Antioxidant, Anti-Inflammatory, and Enzyme Inhibitory Activities of an Endemic Species from Southern Algeria: Warionia saharae. PMID:34500690
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. PMID:34496225
Structural and biochemical characterization of the novel serpin Iripin-5 from Ixodes ricinus. PMID:34473088
Best Practices for Alchemical Free Energy Calculations [Article v1.0]. PMID:34458687
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes. PMID:34458447
Synthesis and Cytotoxic Activity of Combretastatin A-4 and 2,3-Diphenyl-2H-indazole Hybrids. PMID:34451912
Predicting functional consequences of mutations using molecular interaction network features. PMID:34432150
Ankyrin repeats in context with human population variation. PMID:34428215
Repurposing the estrogen receptor modulator raloxifene to treat SARS-CoV-2 infection. PMID:34404919
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. PMID:34395534
Novel High Affinity Sigma-1 Receptor Ligands from Minimal Ensemble Docking-Based Virtual Screening. PMID:34360878
New Hybrid Compounds Combining Fragments of Usnic Acid and Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibition. PMID:34356597
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database. PMID:34354820
CCD2: design constructs for protein expression, the easy way. PMID:34342272
Structure-based virtual screening suggests inhibitors of 3-Chymotrypsin-Like Protease of SARS-CoV-2 from Vernonia amygdalina and Occinum gratissimum. PMID:34332348
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
Targeting SARS-CoV-2 nonstructural protein 15 endoribonuclease: an in silico perspective. PMID:34290822
Gold(I) Complexes with a Quinazoline Carboxamide Alkynyl Ligand: Synthesis, Cytotoxicity, and Mechanistic Studies. PMID:34248416
Updated SARS-CoV-2 single nucleotide variants and mortality association. PMID:34245452
Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study. PMID:34236527
The Role of MacroH2A Histone Variants in Cancer. PMID:34203934
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism. PMID:34192090
Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines. PMID:34181904
Novel adenosine derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective. PMID:34165771
The American lobster genome reveals insights on longevity, neural, and immune adaptations. PMID:34162536
Validating TDP1 as an Inhibition Target for the Development of Chemosensitizers for Camptothecin-Based Chemotherapy Drugs. PMID:34159519
Structure of AMH bound to AMHR2 provides insight into a unique signaling pair in the TGF-β family. PMID:34155118
Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction. PMID:34109211
Bioinformatics Structural and Phylogenetic Characterization of Entamoeba histolytica Alcohol Dehydrogenase 2 (EhADH2). PMID:34103738
β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin? PMID:34093238
PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data. PMID:34081107
Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum. PMID:34076590
UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments. PMID:34076589
Novel Tdp1 Inhibitors Based on Adamantane Connected with Monoterpene Moieties via Heterocyclic Fragments. PMID:34073771
The Moringin/α-CD Pretreatment Induces Neuroprotection in an In Vitro Model of Alzheimer's Disease: A Transcriptomic Study. PMID:34073287
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro. PMID:34047191
Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. PMID:34038562
Ecology and molecular targets of hypermutation in the global microbiome. PMID:34031405
Structural characterization of PaFkbA: A periplasmic chaperone from Pseudomonas aeruginosa. PMID:34025936
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. PMID:34019656
New diarylsulfonamide inhibitors of Leishmania infantum amastigotes. PMID:34015753
Universal Architectural Concepts Underlying Protein Folding Patterns. PMID:33996891
Potential Mechanism Prediction of Herbal Medicine for Pulmonary Fibrosis Associated with SARS-CoV-2 Infection Based on Network Analysis and Molecular Docking. PMID:33986661
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
Structural and biophysical characterization of the nucleosome-binding PZP domain. PMID:33982013
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
From integrative structural biology to cell biology. PMID:33957123
Structural biology in the time of COVID-19: perspectives on methods and milestones. PMID:33953920
Validation of the Crystallography Open Database using the Crystallographic Information Framework. PMID:33953659
The Protein Data Bank Archive. PMID:33950382
The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors. PMID:33927258
A novel KCNQ4 gene variant (c.857A>G; p.Tyr286Cys) in an extended family with non‑syndromic deafness 2A. PMID:33846771
A mathematical representation of protein binding sites using structural dispersion of atoms from principal axes for classification of binding ligands. PMID:33831020
Adaptive Cartesian and torsional restraints for interactive model rebuilding. PMID:33825704
Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors. PMID:33808389
Atomic Structure of the Trichomonas vaginalis Double-Stranded RNA Virus 2. PMID:33785622
How the Protein Data Bank changed biology: An introduction to the JBC Reviews thematic series, part 1. PMID:33785358
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. PMID:33779550
ATP signaling in the integrative neural center of Aplysia californica. PMID:33750901
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae. PMID:33686077
Generative Adversarial Learning of Protein Tertiary Structures. PMID:33668217
New 3-Aryl-2-(2-thienyl)acrylonitriles with High Activity Against Hepatoma Cells. PMID:33668139
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
Exploring the mechanisms underlying the therapeutic effect of Salvia miltiorrhiza in diabetic nephropathy using network pharmacology and molecular docking. PMID:33634308
Therapeutic Lowering of C-Reactive Protein. PMID:33633738
Inhibiting HTLV-1 Protease: A Viable Antiviral Target. PMID:33619959
Catalpol Protects Against Pulmonary Fibrosis Through Inhibiting TGF-β1/Smad3 and Wnt/β-Catenin Signaling Pathways. PMID:33584272
Computational search for drug repurposing to identify potential inhibitors against SARS-COV-2 using Molecular Docking, QTAIM and IQA methods in viral Spike protein - Human ACE2 interface. PMID:33583954
NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13C- and Uniformly 100% 15N-Labeled Sample. PMID:33535444
NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins. PMID:33514717
ProMod3-A versatile homology modelling toolbox. PMID:33507980
Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188. PMID:33503819
A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. PMID:33495445
Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF. PMID:33495441
Antioxidant and Antiproliferative Activity of The Ethanolic Extract of Equisetum Myriochaetum and Molecular Docking of Its Main Metabolites (Apigenin, Kaempferol, and Quercetin) on β-Tubulin. PMID:33466999
Improving SARS-CoV-2 structures: Peer review by early coordinate release. PMID:33460600
Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation. PMID:33453989
Polinton-like viruses are abundant in aquatic ecosystems. PMID:33436089
A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors. PMID:33406218
A systematic analysis of the beta hairpin motif in the Protein Data Bank. PMID:33389765
N-Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides: Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents. PMID:33375766
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. PMID:33339190
A multiscale coarse-grained model of the SARS-CoV-2 virion. PMID:33253634
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases. PMID:33187094
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
A review on drug repurposing applicable to COVID-19. PMID:33147623
Pfam: The protein families database in 2021. PMID:33125078
PDB-tools web: A user-friendly interface for the manipulation of PDB files. PMID:33111403
Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2. PMID:33101264
Towards Dissecting the Mechanism of Protein Phosphatase-1 Inhibition by Its C-Terminal Phosphorylation. PMID:33085143
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PMID:33075050
Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity. PMID:33060678
During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing. PMID:33057423
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models. PMID:33055034
Single Residue Variation in Skeletal Muscle Myosin Enables Direct and Selective Drug Targeting for Spasticity and Muscle Stiffness. PMID:33035452
The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme. PMID:32998385
Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog. PMID:32988830
Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia. PMID:32942984
Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2. PMID:32938504
Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. PMID:32914530
Functional Characterization of the Pseudomonas aeruginosa Ribosome Hibernation-Promoting Factor. PMID:32900865
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. PMID:32881101
p53 tetramerization: at the center of the dominant-negative effect of mutant p53. PMID:32873579
Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α-Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X-ray Scattering and Variational Bayesian Weighting. PMID:32866007
Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics. PMID:32857965
Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway. PMID:32840360
Sodium action potentials in placozoa: Insights into behavioral integration and evolution of nerveless animals. PMID:32828537
A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. PMID:32804373
Isolating structural errors in reaction networks in systems biology. PMID:32790862
Effect of sodium butyrate on HDAC8 mRNA expression in colorectal cancer cell lines and molecular docking study of LHX1 - sodium butyrate interaction. PMID:32788915
Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus. PMID:32787141
A chemical interpretation of protein electron density maps in the worldwide protein data bank. PMID:32785279
Potential mechanism prediction of Cold-Damp Plague Formula against COVID-19 via network pharmacology analysis and molecular docking. PMID:32754224
The Human TSHβ Subunit Proteins and Their Binding Sites on the TSH Receptor Using Molecular Dynamics Simulation. PMID:32738139
Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins. PMID:32733087
Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. PMID:32728686
Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. PMID:32719506
Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. PMID:32713863
Side chain flexibility and the symmetry of protein homodimers. PMID:32706779
The data universe of structural biology. PMID:32695409
Delving deep into the structural aspects of a furin cleavage site inserted into the spike protein of SARS-CoV-2: A structural biophysical perspective. PMID:32622243
Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. PMID:32620933
The maturase HydF enables [FeFe] hydrogenase assembly via transient, cofactor-dependent interactions. PMID:32620553
Signature-based approaches for informed drug repurposing: targeting CNS disorders. PMID:32604402
Predicting the Effect of Chemical Factors on the pH of Crystallization Trials. PMID:32540772
Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach. PMID:32521680
1,2,3-Triazolylmethaneboronate: A Structure Activity Relationship Study of a Class of β-Lactamase Inhibitors against Acinetobacter baumannii Cephalosporinase. PMID:32502340
Femtosecond-to-millisecond structural changes in a light-driven sodium pump. PMID:32499654
Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. PMID:32498246
Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. PMID:32434930
The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans. PMID:32408858
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering. PMID:32397410
Structure of the SARS-Unique Domain C From the Bat Coronavirus HKU4. PMID:32395093
ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam. PMID:32381789
Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs. PMID:32379896
Entropy, Fluctuations, and Disordered Proteins. PMID:32336912
Characterizing human odorant signals: insights from insect semiochemistry and in silico modelling. PMID:32306882
Ebola virus glycoprotein GP1-host cell-surface HSPA5 binding site prediction. PMID:32291698
System Approach for Building of Calcium-Binding Sites in Proteins. PMID:32290360
Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. PMID:32231015
Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. PMID:32222463
Defining the subcellular distribution and metabolic channeling of phosphatidylinositol. PMID:32211894
Small protein folds at the root of an ancient metabolic network. PMID:32188785
Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo-Electron Microscopy Maps. PMID:32187813
COVID-19 spike-host cell receptor GRP78 binding site prediction. PMID:32169481
Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2. PMID:32144209
Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection. PMID:32143444
Optimizing the refinement of merohedrally twinned P61 HIV-1 protease-inhibitor cocrystal structures. PMID:32133994
Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. PMID:32119961
Protein X-ray Crystallography and Drug Discovery. PMID:32106588
Self-organized emergence of folded protein-like network structures from geometric constraints. PMID:32106258
What are the current limits on determination of protonation state using neutron macromolecular crystallography? PMID:32093835
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
Loss of phosphatase activity in PTEN (phosphatase and tensin homolog deleted on chromosome ten) results in endometrial carcinoma in humans: An in-silico study. PMID:32042934
BioMagResBank (BMRB) as a Resource for Structural Biology. PMID:32006287
A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications. PMID:31960607
Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases. PMID:31949901
RGD-hirudin-based low molecular weight peptide prevents blood coagulation via subcutaneous injection. PMID:31949293
Propensities of Amino Acid Pairings in Secondary Structure of Globular Proteins. PMID:31933010
Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes. PMID:31906171
Structural insights revealed by two novel THRB mutations. PMID:31902113
Effect of Reaction Temperature on Shape Evolution of Palladium Nanoparticles and Their Cytotoxicity against A-549 Lung Cancer Cells. PMID:31891061
Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy. PMID:31878088
Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer. PMID:31857588
The CC' loop of IgV domains of the immune checkpoint receptors, plays a key role in receptor:ligand affinity modulation. PMID:31844079
Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. PMID:31819058
Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. PMID:31817975
Discovery and Characterisation of Dual Inhibitors of Tryptophan 2,3-Dioxygenase (TDO2) and Indoleamine 2,3-Dioxygenase 1 (IDO1) Using Virtual Screening. PMID:31795096
Dissecting the role of novel EZH2 inhibitors in primary glioblastoma cell cultures: effects on proliferation, epithelial-mesenchymal transition, migration, and on the pro-inflammatory phenotype. PMID:31791385
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination. PMID:31777934
Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. PMID:31767868
A New Look at the Structures of Old Sepsis Actors by Exploratory Data Analysis Tools. PMID:31739644
Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood. PMID:31731771
Data-Driven Materials Science: Status, Challenges, and Perspectives. PMID:31728276
New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. PMID:31724275
Identification of Isoform-Selective Ligands for the Middle Domain of Heat Shock Protein 90 (Hsp90). PMID:31717777
Curcumin Derivatives Verify the Essentiality of ROS Upregulation in Tumor Suppression. PMID:31717651
Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. PMID:31712588
Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. PMID:31661858
Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. PMID:31645552
Structure and Dynamics of a Site-Specific Labeled Fc Fragment with Altered Effector Functions. PMID:31640157
Pentagamavunon-1 (PGV-1) inhibits ROS metabolic enzymes and suppresses tumor cell growth by inducing M phase (prometaphase) arrest and cell senescence. PMID:31619723
New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors. PMID:31619021
Unsupervised and Supervised Learning over theEnergy Landscape for Protein Decoy Selection. PMID:31615116
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
The C-terminal region of human plasma fetuin-B is dispensable for the raised-elephant-trunk mechanism of inhibition of astacin metallopeptidases. PMID:31604990
A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes. PMID:31603792
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Acceleration and Parallelization of ZENO/Walk-on-Spheres. PMID:31579292
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer. PMID:31548583
Leucine 232 and hydrophobic residues at the ribosomal P stalk binding site are critical for biological activity of ricin. PMID:31548364
Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms. PMID:31546607
Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents. PMID:31537789
New insights and innovation from a million crystal structures in the Cambridge Structural Database. PMID:31489338
Structure-Based Screening of Tetrazolylhydrazide Inhibitors versus KDM4 Histone Demethylases. PMID:31475772
Novel guanosine derivatives against Zika virus polymerase in silico. PMID:31436327
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. PMID:31427836
Cryo-EM structure of the native rhodopsin dimer in nanodiscs. PMID:31399513
Identifying potential novel drugs against Helicobacter pylori by targeting the essential response regulator HsrA. PMID:31383920
Estimating dispensable content in the human interactome. PMID:31324802
Archiving and disseminating integrative structure models. PMID:31278630
Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. PMID:31274415
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. PMID:31257108
Recombinant production, purification, crystallization, and structure analysis of human transforming growth factor β2 in a new conformation. PMID:31209258
Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. PMID:31207330
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Metabolic and Epigenetic Action Mechanisms of Antidiabetic Medicinal Plants. PMID:31191707
Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study. PMID:31179358
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. PMID:31172379
Sequence-specific dynamic information in proteins. PMID:31134683
Structural basis of resistance of mutant RET protein-tyrosine kinase to its inhibitors nintedanib and vandetanib. PMID:31118272
In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. PMID:31101900
Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein. PMID:31067727
Novel T9 loop conformation of filamenting temperature-sensitive mutant Z from Mycobacterium tuberculosis. PMID:31045565
Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5. PMID:31045561
Configurational Entropy Components and Their Contribution to Biomolecular Complex Formation. PMID:31042036
MIReAD, a minimum information standard for reporting arthropod abundance data. PMID:31024009
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction. PMID:31023237
Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders. PMID:31013090
An algebraic language for RNA pseudoknots comparison. PMID:30999864
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PMID:30986271
The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework. PMID:30975904
Mathematical modeling in cancer nanomedicine: a review. PMID:30949850
A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius. PMID:30948713
Molecular evolution of Pr1 proteases depicts ongoing diversification in Metarhizium spp. PMID:30923942
Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins. PMID:30923664
Anticipating innovations in structural biology. PMID:30912485
The three-dimensional structure and recognition mechanism of Manduca sexta peptidoglycan recognition protein-1. PMID:30905759
Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor. PMID:30894633
Essay on Biomembrane Structure. PMID:30877332
Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations. PMID:30872635
Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition. PMID:30867929
Vasodilation Elicited by Isoxsuprine, Identified by High-Throughput Virtual Screening of Compound Libraries, Involves Activation of the NO/cGMP and H₂S/KATP Pathways and Blockade of α₁-Adrenoceptors and Calcium Channels. PMID:30862086
Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. PMID:30834751
Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities. PMID:30834312
Processivity vs. Beating: Comparing Cytoplasmic and Axonemal Dynein Microtubule Binding Domain Association with Microtubule. PMID:30832428
Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction. PMID:30823390
Structural Determinants of Isoform Selectivity in PI3K Inhibitors. PMID:30813656
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PMID:30794542
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. PMID:30784590
NMR model structure of the antimicrobial peptide maximin 3. PMID:30734844
GlyStruct: glycation prediction using structural properties of amino acid residues. PMID:30717650
Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals. PMID:30713701
Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome. PMID:30698743
Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis - An Insight Into the Zinc Homeostasis of the Pathogen. PMID:30687290
Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation. PMID:30648154
Do Antimicrobial Proteins Contribute to Overcoming the Hidden Antifungal Crisis at the Dawn of a Post-Antibiotic Era? PMID:30641886
B-factor Guided Proline Substitutions in Chromobacterium violaceum Amine Transaminase: Evaluation of the Proline Rule as a Method for Enzyme Stabilization. PMID:30637901
The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis. PMID:30621735
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Synthesis, Biological Evaluation and Docking Studies of Benzoxazoles Derived from Thymoquinone. PMID:30545123
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
Dynamics based clustering of globin family members. PMID:30513111
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. PMID:30416256
High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure. PMID:30387765
Using a Consensus Docking Approach to Predict Adverse Drug Reactions in Combination Drug Therapies for Gulf War Illness. PMID:30373189
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
The Pfam protein families database in 2019. PMID:30357350
Multi-criteria protein structure comparison and structural similarities analysis using pyMCPSC. PMID:30332415
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Structure of the Recombinant Neisseria gonorrhoeae Adhesin Complex Protein (rNg-ACP) and Generation of Murine Antibodies with Bactericidal Activity against Gonococci. PMID:30305317
Impact of structural prior knowledge in SNV prediction: Towards causal variant finding in rare disease. PMID:30265692
From mutations to mechanisms and dysfunction via computation and mining of protein energy landscapes. PMID:30255791
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
Functional classification of long non-coding RNAs by k-mer content. PMID:30224646
Structural models of the NaPi-II sodium-phosphate cotransporters. PMID:30175376
The calcium-binding site of human glutamate carboxypeptidase II is critical for dimerization, thermal stability, and enzymatic activity. PMID:30168215
Development of NMR and thermal shift assays for the evaluation of Mycobacterium tuberculosis isocitrate lyase inhibitors. PMID:30108733
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. PMID:30054521
Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. PMID:30054360
Digital open science-Teaching digital tools for reproducible and transparent research. PMID:30048447
Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3). PMID:30022031
Structural Biology Helps Interpret Variants of Uncertain Significance in Genes Causing Endocrine and Metabolic Disorders. PMID:30019023
Computational analysis of kinase inhibitor selectivity using structural knowledge. PMID:29985971
SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PMID:29975698
NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione. PMID:29923039
Investigation of protein quaternary structure via stoichiometry and symmetry information. PMID:29864163
Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. PMID:29863194
Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy. PMID:29799751
Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. PMID:29782488
Targeting G protein-coupled receptor signaling at the G protein level with a selective nanobody inhibitor. PMID:29777099
A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model. PMID:29765606
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Functional Cross-Talk between Adenosine and Metabotropic Glutamate Receptors. PMID:29663888
Structural analysis of glycoproteins: building N-linked glycans with Coot. PMID:29652253
Expression profiles of TRPV1, TRPV4, TLR4 and ERK1/2 in the dorsal root ganglionic neurons of a cancer-induced neuropathy rat model. PMID:29637027
MoleculeNet: a benchmark for molecular machine learning. PMID:29629118
Structure and evolution of the Fam20 kinases. PMID:29572475
Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. PMID:29562592
Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. PMID:29562181
Structural insights of dipeptidyl peptidase-IV inhibitors through molecular dynamics-guided receptor-dependent 4D-QSAR studies. PMID:29536226
Model validation: local diagnosis, correction and when to quit. PMID:29533239
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. PMID:29533225
Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters. PMID:29520356
Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark. PMID:29517771
The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. PMID:29487617
Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands. PMID:29473857
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. PMID:29409446
EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures. PMID:29391170
Coumarin: A Natural, Privileged and Versatile Scaffold for Bioactive Compounds. PMID:29382051
Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. PMID:29377002
Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate. PMID:29372894
From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction. PMID:29351266
"In Silico" Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger. PMID:29348934
Investigation into Improving the Aqueous Solubility of the Thieno[2,3-b]pyridine Anti-Proliferative Agents. PMID:29324695
Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring. PMID:29288899
GPCR Modulation of Thieno[2,3-b]pyridine Anti-Proliferative Agents. PMID:29258235
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
Identification of Clinically Approved Drugs Indacaterol and Canagliflozin for Repurposing to Treat Epidermal Growth Factor Tyrosine Kinase Inhibitor-Resistant Lung Cancer. PMID:29238696
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. PMID:29190272
Validation of Structures in the Protein Data Bank. PMID:29174494
To what extent do structural changes in catalytic metal sites affect enzyme function? PMID:29161638
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Analysis of the conformations of the HIV-1 protease from a large crystallographic data set. PMID:29124093
Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank. PMID:29103094
Synthesis and Biological Evaluation of 2H-Indazole Derivatives: Towards Antimicrobial and Anti-Inflammatory Dual Agents. PMID:29088121
Prolyl dihydroxylation of unassembled uS12/Rps23 regulates fungal hypoxic adaptation. PMID:29083304
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
ChannelsDB: database of biomacromolecular tunnels and pores. PMID:29036719
Protein microcrystallography using synchrotron radiation. PMID:28989710
Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671. PMID:28965821
A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of Proteus mirabilis. PMID:28949977
AUSPEX: a graphical tool for X-ray diffraction data analysis. PMID:28876236
Rules for connectivity of secondary structure elements in protein: Two-layer αβ sandwiches. PMID:28856751
Expression, Docking, and Molecular Dynamics of Endo-β-1,4-xylanase I Gene of Trichoderma virens in Pichia stipitis. PMID:28856159
Modeling of RAS complexes supports roles in cancer for less studied partners. PMID:28815022
The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. PMID:28814505
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. PMID:28811629
Multifunctional Cinnamic Acid Derivatives. PMID:28757554
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. PMID:28732462
UCSF ChimeraX: Meeting modern challenges in visualization and analysis. PMID:28710774
Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. PMID:28683550
Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. PMID:28680402
Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. PMID:28664878
Trichoderma virens β-glucosidase I (BGLI) gene; expression in Saccharomyces cerevisiae including docking and molecular dynamics studies. PMID:28637443
Potential inhibitory effect of indolizine derivatives on the two enzymes: nicotinamide phosphoribosyltransferase and beta lactamase, a molecular dynamics study. PMID:28634829
S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. PMID:28629859
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein? PMID:28570645
A rapid expression and purification condition screening protocol for membrane protein structural biology. PMID:28543736
Proteins in binary solvents. PMID:28510051
In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species. PMID:28487711
Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone. PMID:28481092
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. PMID:28472402
ProteinsPlus: a web portal for structure analysis of macromolecules. PMID:28472372
Is Polysialylated NCAM Not Only a Regulator during Brain Development But also during the Formation of Other Organs? PMID:28448440
The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein. PMID:28375705
PDB2CD visualises dynamics within protein structures. PMID:28374045
Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore. PMID:28369612
Towards an efficient compression of 3D coordinates of macromolecular structures. PMID:28362865
Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites. PMID:28345007
Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. PMID:28336403
WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design. PMID:28291763
Proper modelling of ligand binding requires an ensemble of bound and unbound states. PMID:28291761
Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis. PMID:28291758
Tools for ligand validation in Coot. PMID:28291755
Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. PMID:28289214
Data archiving and availability in an era of open science. PMID:28250935
Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk. PMID:28230053
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive. PMID:28216043
Proteins analysed as virtual knots. PMID:28205562
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. PMID:28178937
Glycoblocks: a schematic three-dimensional representation for glycans and their interactions. PMID:28177314
Ligand fitting with CCP4. PMID:28177312
Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes. PMID:28177305
Guidelines for the successful generation of protein-ligand complex crystals. PMID:28177304
A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic. PMID:28154188
Protein Bioinformatics Databases and Resources. PMID:28150231
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Docking into Mycobacterium tuberculosis Thioredoxin Reductase Protein Yields Pyrazolone Lead Molecules for Methicillin-Resistant Staphylococcus aureus. PMID:28134858
Crystal structure of a putrescine aminotransferase from Pseudomonas sp. strain AAC. PMID:28045391
Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. PMID:28036383
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
Uniclust databases of clustered and deeply annotated protein sequences and alignments. PMID:27899574
Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets. PMID:27862010
Similarity search for local protein structures at atomic resolution by exploiting a database management system. PMID:27857569
A public database of macromolecular diffraction experiments. PMID:27841751
Resolution of ab initio shapes determined from small-angle scattering. PMID:27840683
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. PMID:27803746
Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase. PMID:27801788
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6. PMID:27756822
Benefits of Multifaceted Chemopreventives in the Suppression of the Oral Squamous Cell Carcinoma (OSCC) Tumorigenic Phenotype. PMID:27756753
Coumarin Antifungal Lead Compounds from Millettia thonningii and Their Predicted Mechanism of Action. PMID:27754464
Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones. PMID:27736955
Identifying and Visualizing Macromolecular Flexibility in Structural Biology. PMID:27668215
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. PMID:27618147
Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces. PMID:27611671
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. PMID:27599738
Databases and Archiving for CryoEM. PMID:27572735
Computing energy landscape maps and structural excursions of proteins. PMID:27535545
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
The Need for Integrated Approaches in Metabolic Engineering. PMID:27527588
HLA-B*51:01 is strongly associated with clindamycin-related cutaneous adverse drug reactions. PMID:27527109
HOMCOS: an updated server to search and model complex 3D structures. PMID:27522608
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis. PMID:27506766
Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. PMID:27497175
Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins. PMID:27493859
Distinct Conformation of ATP Molecule in Solution and on Protein. PMID:27493535
Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria. PMID:27458784
The archiving and dissemination of biological structure data. PMID:27450113
Examining the Conservation of Kinks in Alpha Helices. PMID:27314675
DCC: a Swiss army knife for structure factor analysis and validation. PMID:27275151
Protease Inhibitors in View of Peptide Substrate Databases. PMID:27247997
Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase. PMID:27242998
A Novel Variant in CMAH Is Associated with Blood Type AB in Ragdoll Cats. PMID:27171395
Characterization of activating mutations of NOTCH3 in T-cell acute lymphoblastic leukemia and anti-leukemic activity of NOTCH3 inhibitory antibodies. PMID:27157619
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PMID:27124275
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis. PMID:27107576
Calmodulin Promotes N-BAR Domain-Mediated Membrane Constriction and Endocytosis. PMID:27093085
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
Thiol-Disulfide Exchange Reactions in the Mammalian Extracellular Environment. PMID:27023663
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. PMID:26988596
The FAIR Guiding Principles for scientific data management and stewardship. PMID:26978244
An extended set of yeast-based functional assays accurately identifies human disease mutations. PMID:26975778
A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error. PMID:26960124
Data publication with the structural biology data grid supports live analysis. PMID:26947396
Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage. PMID:26924271
Molecular determinants and interaction data of cyclic peptide inhibitor with the extracellular domain of TrkB receptor. PMID:26909388
L-Hydroxyproline and d-Proline Catabolism in Sinorhizobium meliloti. PMID:26833407
The solution structure of the kallikrein-related peptidases inhibitor SPINK6. PMID:26828269
Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases. PMID:26749496
Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments. PMID:26745406
The structure of a prophenoloxidase (PPO) from Anopheles gambiae provides new insights into the mechanism of PPO activation. PMID:26732497
Smiles2Monomers: a link between chemical and biological structures for polymers. PMID:26715946
Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases. PMID:26709959
Crystallographic education in the 21st century. PMID:26664347
Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold. PMID:26572934
Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. PMID:26527733
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
High-resolution structures of Lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate. PMID:26457526
Towards predictive docking at aminergic G-protein coupled receptors. PMID:26453085
Regulation of the Target of Rapamycin and Other Phosphatidylinositol 3-Kinase-Related Kinases by Membrane Targeting. PMID:26426064
Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins. PMID:26404256
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PMID:26325505
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Multiple Surface Regions on the Niemann-Pick C2 Protein Facilitate Intracellular Cholesterol Transport. PMID:26296895
In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug. PMID:26147897
Structural basis of the broadly neutralizing anti-interferon-α antibody rontalizumab. PMID:26099203
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. PMID:26095030
The Caltech Tomography Database and Automatic Processing Pipeline. PMID:26087141
The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. PMID:26071966
Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides. PMID:26023288
A less-biased analysis of metalloproteins reveals novel zinc coordination geometries. PMID:26009987
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. PMID:25982853
The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology. PMID:25942442
High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics. PMID:25894612
Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. PMID:25849403
Structure of the N-terminal domain of the protein Expansion: an 'Expansion' to the Smad MH2 fold. PMID:25849395
Protein domain-level landscape of cancer-type-specific somatic mutations. PMID:25794154
Identifying and quantifying radiation damage at the atomic level. PMID:25723922
Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin. PMID:25694384
Models of protein-ligand crystal structures: trust, but verify. PMID:25665575
Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli aminopeptidase N. PMID:25644575
Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. PMID:25619999
A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. PMID:25615961
An approach to creating a more realistic working model from a protein data bank entry. PMID:25605595
The origin of CDR H3 structural diversity. PMID:25579815
Identification of FAH domain-containing protein 1 (FAHD1) as oxaloacetate decarboxylase. PMID:25575590
You are lost without a map: Navigating the sea of protein structures. PMID:25554228
OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION. PMID:25552783
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. PMID:25540181
Protein structure annotation resources. PMID:25502191
Multitarget molecular hybrids of cinnamic acids. PMID:25474291
Structure-function analysis of vaccinia virus H7 protein reveals a novel phosphoinositide binding fold essential for poxvirus replication. PMID:25473060
A general computational approach for repeat protein design. PMID:25451037
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
Biochemical and structural characterization of the apicoplast dihydrolipoamide dehydrogenase of Plasmodium falciparum. PMID:25387830
A series of PDB-related databanks for everyday needs. PMID:25352545
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action. PMID:25324859
The lipid cubic phase or in meso method for crystallizing proteins. Bushings for better manual dispensing. PMID:25294983
A 3D cellular context for the macromolecular world. PMID:25289590
Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure. PMID:25286936
How to make deposition of images a reality. PMID:25286838
Determination of protein-ligand interactions using differential scanning fluorimetry. PMID:25285605
Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus. PMID:25285205
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. PMID:25183487
Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study. PMID:25159129
A splicing mutation in the novel mitochondrial protein DNAJC11 causes motor neuron pathology associated with cristae disorganization, and lymphoid abnormalities in mice. PMID:25111180
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. PMID:25075337
The Protein Data Bank archive as an open data resource. PMID:25062767
Novel cinnamic acid derivatives as antioxidant and anticancer agents: design, synthesis and modeling studies. PMID:25004073
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research. PMID:24932210
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family. PMID:24920445
Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. PMID:24914984
Computational evaluation of factors governing catalytic 2-keto acid decarboxylation. PMID:24912593
Drawing the PDB: Protein-Ligand Complexes in Two Dimensions. PMID:24900245
BRCA1 point mutations in premenopausal breast cancer patients from Central Sudan. PMID:24729269
The histone-fold complex MHF is remodeled by FANCM to recognize branched DNA and protect genome stability. PMID:24699063
Exploring the biological and chemical complexity of the ligases. PMID:24657765
Data management in the modern structural biology and biomedical research environment. PMID:24590705
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method. PMID:24565158
A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction. PMID:24565020
Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. PMID:24519881
Data sharing policy design for consortia: challenges for sustainability. PMID:24475754
istar: a web platform for large-scale protein-ligand docking. PMID:24475049
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. PMID:24470572
Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset. PMID:24458507
Acceleration of an aromatic Claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad. PMID:24456160
Automating crystallographic structure solution and refinement of protein-ligand complexes. PMID:24419387
Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. PMID:24416252
A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. PMID:24366729
Structural basis for the design of selective phosphodiesterase 4B inhibitors. PMID:24361374
Tat peptide-mediated soluble expression of the membrane protein LSECtin-CRD in Escherichia coli. PMID:24358298
LigSearch: a knowledge-based web server to identify likely ligands for a protein target. PMID:24311580
Timely deposition of macromolecular structures is necessary for peer review. PMID:24311569
Chemical annotation of small and peptide-like molecules at the Protein Data Bank. PMID:24291661
PDBe: Protein Data Bank in Europe. PMID:24288376
Phaser.MRage: automated molecular replacement. PMID:24189240
The Nucleic Acid Database: new features and capabilities. PMID:24185695
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. PMID:24173824
PDBsum additions. PMID:24153109
The strawberry pathogenesis-related 10 (PR-10) Fra a proteins control flavonoid biosynthesis by binding to metabolic intermediates. PMID:24133217
Discovery of a new genetic variant of methionine aminopeptidase from Streptococci with possible post-translational modifications: biochemical and structural characterization. PMID:24124477
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. PMID:24113529
How community has shaped the Protein Data Bank. PMID:24010707
LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory. PMID:23935832
Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase. PMID:23915572
Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus. PMID:23902280
On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin. PMID:23897468
Network model of a protein globule. PMID:23897064
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis. PMID:23722833
A novel protocol for three-dimensional structure prediction of RNA-protein complexes. PMID:23712416
A combined 3D-QSAR and docking studies for the In-silico prediction of HIV-protease inhibitors. PMID:23683267
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
OpenStructure: an integrated software framework for computational structural biology. PMID:23633579
CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. PMID:23621914
Soluble polysialylated NCAM: a novel player of the innate immune system in the lung. PMID:23619613
Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins. PMID:23602661
Structure of a filament of stacked octamers of human DMC1 recombinase. PMID:23545642
Functional site plasticity in domain superfamilies. PMID:23499848
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. PMID:23493556
Activation of ATP binding for the autophosphorylation of DosS, a Mycobacterium tuberculosis histidine kinase lacking an ATP lid motif. PMID:23486471
Alignment of helical membrane protein sequences using AlignMe. PMID:23469223
Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. PMID:23451892
Classifying the metal dependence of uncharacterized nitrogenases. PMID:23440025
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. PMID:23341755
A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis. PMID:23337983
Trendspotting in the Protein Data Bank. PMID:23337870
Protein data bank. PMID:23326114
Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis. PMID:23295488
Fibrin clot structure and mechanics associated with specific oxidation of methionine residues in fibrinogen. PMID:23283239
Using RosettaLigand for small molecule docking into comparative models. PMID:23239984
Data management challenges in three-dimensional EM. PMID:23211764
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
CDD: conserved domains and protein three-dimensional structure. PMID:23197659
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118. PMID:23192019
Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio. PMID:23151633
PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides. PMID:23151233
An assignment of intrinsically disordered regions of proteins based on NMR structures. PMID:23142703
The human "magnesome": detecting magnesium binding sites on human proteins. PMID:23095498
Cloning, expression and functional validation of drought inducible ascorbate peroxidase (Ec-apx1) from Eleusine coracana. PMID:23065288
The future of the Protein Data Bank. PMID:23023942
Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. PMID:23011872
CING: an integrated residue-based structure validation program suite. PMID:22986687
Creating a community resource for protein science. PMID:22969036
QUAFIT: a novel method for the quaternary structure determination from small-angle scattering data. PMID:22947867
Nanoinformatics: developing new computing applications for nanomedicine. PMID:22942787
The methionine-aromatic motif plays a unique role in stabilizing protein structure. PMID:22859300
Ser/Thr motifs in transmembrane proteins: conservation patterns and effects on local protein structure and dynamics. PMID:22836667
Putting proteins in context: scientific illustrations bring together information from diverse sources to provide an integrative view of the molecular biology of cells. PMID:22806423
Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface. PMID:22759582
Public domain databases for medicinal chemistry. PMID:22731701
Biosynthesis of the tunicamycin antibiotics proceeds via unique exo-glycal intermediates. PMID:22717438
An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation. PMID:22706892
Structure of a hexameric form of RadA recombinase from Methanococcus voltae. PMID:22691778
Invertebrate lysozymes: diversity and distribution, molecular mechanism and in vivo function. PMID:22581338
Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana. PMID:22549903
Mutagenesis of the bovSERPINA3-3 demonstrates the requirement of aspartate-371 for intermolecular interaction and formation of dimers. PMID:22505318
PDB_REDO: constructive validation, more than just looking for errors. PMID:22505269
Handling ligands with Coot. PMID:22505262
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. PMID:22505258
Research priorities. Shining light into black boxes. PMID:22499926
Identification of novel liver X receptor activators by structure-based modeling. PMID:22489742
PDB_REDO: automated re-refinement of X-ray structure models in the PDB. PMID:22477769
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. PMID:22476577
Highlights from recently determined structures of membrane proteins: a focus on channels and transporters. PMID:22472602
The transcription factor encyclopedia. PMID:22458515
Glu121-Lys319 salt bridge between catalytic and N-terminal domains is pivotal for the activity and stability of Escherichia coli aminopeptidase N. PMID:22411732
The Protein Data Bank at 40: reflecting on the past to prepare for the future. PMID:22404998
Prediction of dinucleotide-specific RNA-binding sites in proteins. PMID:22373260
An interview with Phil Bourne, associate director of the RCSB protein data bank. PMID:22366956
Prediction of HIV-1 protease/inhibitor affinity using RosettaLigand. PMID:22321894
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. PMID:22260278
Novel search method for the discovery of functional relationships. PMID:22180409
Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. PMID:22180049
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. PMID:22139937
Celebrating structural biology. PMID:22139036
PDBe: Protein Data Bank in Europe. PMID:22110033
MACiE: exploring the diversity of biochemical reactions. PMID:22058127
Amphipathic properties of HIV-1 gp41 fusion inhibitors. PMID:22044226
Pharmacophore-based discovery of FXR agonists. Part I: Model development and experimental validation. PMID:22018919
Pharmacophore-based discovery of FXR-agonists. Part II: identification of bioactive triterpenes from Ganoderma lucidum. PMID:22014750
ViPR: an open bioinformatics database and analysis resource for virology research. PMID:22006842
A new generation of crystallographic validation tools for the protein data bank. PMID:22000512
CASP9 target classification. PMID:21997778
Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods. PMID:21966510
Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. PMID:21904052
Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. PMID:21904051
The Protein Maker: an automated system for high-throughput parallel purification. PMID:21904043
Structural genomics of infectious disease drug targets: the SSGCID. PMID:21904037
Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone. PMID:21901122
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr. PMID:21796434
The cytoplasmic rhodopsin-protein interface: potential for drug discovery. PMID:21777183
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. PMID:21752305
Modelling of lysozyme binding to a cation exchange surface at atomic detail: the role of flexibility. PMID:21689536
Structural determinants of limited proteolysis. PMID:21682278
Disulfide scrambling in IgG2 monoclonal antibodies: insights from molecular dynamics simulations. PMID:21671135
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models. PMID:21665925
An Update on GABAρ Receptors. PMID:21629448
Fractal symmetry of protein interior: what have we learned? PMID:21614471
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. PMID:21605342
The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. PMID:21575214
A versatile method for systematic conformational searches: application to CheY. PMID:21557263
Accuracy of functional surfaces on comparatively modeled protein structures. PMID:21541664
Chemical modifications in therapeutic protein aggregates generated under different stress conditions. PMID:21518762
Remote thioredoxin recognition using evolutionary conservation and structural dynamics. PMID:21481770
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. PMID:21465562
Distributed structure determination at the JCSG. PMID:21460455
The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory. PMID:21460443
Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PMID:21445244
Homology modeling and in silico screening of inhibitors for the substrate binding domain of human Siah2: implications for hypoxia-induced cancers. PMID:21409570
Targeting TLR4 signaling by TLR4 Toll/IL-1 receptor domain-derived decoy peptides: identification of the TLR4 Toll/IL-1 receptor domain dimerization interface. PMID:21402890
CREBBP mutations in relapsed acute lymphoblastic leukaemia. PMID:21390130
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. PMID:21382834
Contribution of hydrophobic interactions to protein stability. PMID:21377472
Protein structure reports in JIMD--an important enhancement of journal scope. PMID:21369958
Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. PMID:21359640
Mapping protein interactions between Dengue virus and its human and insect hosts. PMID:21358811
Side-chain conformational changes upon Protein-Protein Association. PMID:21354429
Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction. PMID:21284850
The effect of a Pro²⁸Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study. PMID:21264483
Validation of arsenic resistance in Bacillus cereus strain AG27 by comparative protein modeling of arsC gene product. PMID:21258851
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex. PMID:21245343
Protein structure databases. PMID:21225378
Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria. PMID:21210973
A combined ligand- and structure-based virtual screening protocol identifies submicromolar PPARγ partial agonists. PMID:21162086
Paramagnetic relaxation assisted docking of a small indole compound in the HIV-1 gp41 hydrophobic pocket. PMID:21155611
Semi-isometric registration of line features for flexible fitting of protein structures. PMID:21124809
A series of PDB related databases for everyday needs. PMID:21071423
Concept and application of a computational vaccinology workflow. PMID:21067549
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. PMID:21059217
ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability. PMID:21052782
A general route for the synthesis of functional, protein-based hydrogel microspheres using tailored protein charge. PMID:21052577
VnD: a structure-centric database of disease-related SNPs and drugs. PMID:21051351
Recovering physical potentials from a model protein databank. PMID:21041685
Ultrasensitive detection and characterization of biomolecules using superchiral fields. PMID:21037572
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison. PMID:20938684
EMDataBank.org: unified data resource for CryoEM. PMID:20935055
The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family. PMID:20934997
Unified data resource for cryo-EM. PMID:20888470
Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences. PMID:20877496
Molecular characterization, structural analysis and determination of host range of a novel bacteriophage LSB-1. PMID:20875143
Predicting cyclooxygenase inhibition by three-dimensional pharmacophoric profiling. Part II: Identification of enzyme inhibitors from Prasaplai, a Thai traditional medicine. PMID:20851587
Myosin cleft closure determines the energetics of the actomyosin interaction. PMID:20837775
OpenStructure: a flexible software framework for computational structural biology. PMID:20733063
Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. PMID:20724439
Sterol binding by OSBP-related protein 1L regulates late endosome motility and function. PMID:20690035
Protein kinase-inhibitor database: structural variability of and inhibitor interactions with the protein kinase P-loop. PMID:20681595
Evaluation and ranking of enzyme designs. PMID:20665693
Update of human and mouse forkhead box (FOX) gene families. PMID:20650821
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. PMID:20639539
Biomolecule analysis by ion mobility spectrometry. PMID:20636082
Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens. PMID:20628623
Generation of MHC class II-peptide ligands for CD4 T-cell allorecognition of MHC class II molecules. PMID:20616724
Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. PMID:20585542
Inhibition of Eimeria tenella CDK-related kinase 2: From target identification to lead compounds. PMID:20575139
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. PMID:20559630
FoXS: a web server for rapid computation and fitting of SAXS profiles. PMID:20507903
A schematic model for molecular affinity and binding with Ising variables. PMID:20480964
Ligand-binding site prediction of proteins based on known fragment-fragment interactions. PMID:20472546
Detection and correction of underassigned rotational symmetry prior to structure deposition. PMID:20445225
Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. PMID:20426868
Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis. PMID:20422267
High-throughput expression and purification of membrane proteins. PMID:20394823
From evidence to inference: probing the evolution of protein interaction networks. PMID:20357887
Community-acquired methicillin-resistant Staphylococcus aureus: community transmission, pathogenesis, and drug resistance. PMID:20336341
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function. PMID:20334658
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PMID:20300652
Glutamine-linked and non-consensus asparagine-linked oligosaccharides present in human recombinant antibodies define novel protein glycosylation motifs. PMID:20233717
Effect of ATP binding and hydrolysis on dynamics of canine parvovirus NS1. PMID:20219935
Molecular interactions between Bos taurus interferon-tau1c and human type I interferon receptor. PMID:20198192
Visualization of omics data for systems biology. PMID:20195258
Visualization of macromolecular structures. PMID:20195256
Visualizing biological data-now and in the future. PMID:20195254
A second actin-like MamK protein in Magnetospirillum magneticum AMB-1 encoded outside the genomic magnetosome island. PMID:20161777
'Hot' macromolecular crystals. PMID:20161694
An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. PMID:20122230
Feasibility of one-shot-per-crystal structure determination using Laue diffraction. PMID:20057043
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Comparative protein modeling, prediction of conserved residue and active sites in cold resistant protein isolated from CRPF(1), a cold tolerant mutant of Pseudomonas fluorescens. PMID:20020303
Structural genomics and drug discovery for infectious diseases. PMID:19860716
High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design. PMID:19851004
Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions. PMID:19834622
Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes. PMID:19812769
RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. PMID:19808808
The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam. PMID:19765305
ZifBASE: a database of zinc finger proteins and associated resources. PMID:19737425
Homology modelling and spectroscopy, a never-ending love story. PMID:19718498
p3d--Python module for structural bioinformatics. PMID:19698094
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
A tool for calculating binding-site residues on proteins from PDB structures. PMID:19650927
Physical basis of metal-binding specificity in Escherichia coli NikR. PMID:19621966
Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution. PMID:19570795
Characterization of wise protein and its molecular mechanism to interact with both Wnt and BMP signals. PMID:19553665
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. PMID:19515936
Sequence conservation in Plasmodium falciparum alpha-helical coiled coil domains proposed for vaccine development. PMID:19492090
Transmembrane protein topology prediction using support vector machines. PMID:19470175
Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. PMID:19362095
Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif. PMID:19286916
Reverse micelles in integral membrane protein structural biology by solution NMR spectroscopy. PMID:19278649
Structural insight into the heme-based redox sensing by DosS from Mycobacterium tuberculosis. PMID:19276084
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution. PMID:19274093
Outcome of a workshop on applications of protein models in biomedical research. PMID:19217386
A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins. PMID:19214496
Instantaneous normal modes and the protein glass transition. PMID:19167298
Data deposition and annotation at the worldwide protein data bank. PMID:19082769
The Protein Model Portal. PMID:19037750
Fibronectin unfolding revisited: modeling cell traction-mediated unfolding of the tenth type-III repeat. PMID:19020673
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
The protein structure initiative structural genomics knowledgebase. PMID:19010965
PDBsum new things. PMID:18996896
Matching curated genome databases: a non trivial task. PMID:18950477
PharmGKB: understanding the effects of individual genetic variants. PMID:18949600
Predicting small ligand binding sites in proteins using backbone structure. PMID:18940825
Ion channel gates: comparative analysis of energy barriers. PMID:18923825
Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures. PMID:18754631
Determining Rieske cluster reduction potentials. PMID:18719951
O2- and NO-sensing mechanism through the DevSR two-component system in Mycobacterium smegmatis. PMID:18708494
Dependence of amino acid side chain 13C shifts on dihedral angle: application to conformational analysis. PMID:18652454
Representation of viruses in the remediated PDB archive. PMID:18645236
Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. PMID:18631376
Influence of nonuniform geometry on nanoindentation of viral capsids. PMID:18621831
Molecular modeling of the axial and circumferential elastic moduli of tubulin. PMID:18621829
Limitations and lessons in the use of X-ray structural information in drug design. PMID:18617015
Discovery of aminoquinolines as a new class of potent inhibitors of heat shock protein 90 (Hsp90): Synthesis, biology, and molecular modeling. PMID:18571929
Ligand preference and orientation in b- and c-type heme-binding proteins. PMID:18491383
soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts. PMID:18487276
Interesting structures: education and outreach at the RCSB Protein Data Bank. PMID:18462020
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. PMID:18442990
On the relevance of defining protein structures in cancer research. PMID:18411193
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. PMID:18391405
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. PMID:18288446
Accurate structural correlations from maximum likelihood superpositions. PMID:18282091
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
Molecular recognition in the sphingosine 1-phosphate receptor family. PMID:18165127
Remediation of the protein data bank archive. PMID:18073189
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
BioMagResBank. PMID:17984079
Glycoconjugate Data Bank: Structures--an annotated glycan structure database and N-glycan primary structure verification service. PMID:17933765
Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. PMID:17888947
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
Solution mapping of T cell receptor docking footprints on peptide-MHC. PMID:17670943
Modeling and analysis of ligand-receptor interactions in the GABAc receptor. PMID:17506348
Evolutionary rates vary among rRNA structural elements. PMID:17468501
The MEPS server for identifying protein conformational epitopes. PMID:17430573
Crystallographic refinement of ligand complexes. PMID:17164531
Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase. PMID:17158155
X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative. PMID:17145714
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. PMID:17142228
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. PMID:17082206
A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PMID:17069453
ORENZA: a web resource for studying ORphan ENZyme activities. PMID:17026747
An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. PMID:17016668
Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus. PMID:17013395
Serine hydrolase KIAA1363: toxicological and structural features with emphasis on organophosphate interactions. PMID:16978018
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. PMID:16972168
Curation of complex, context-dependent immunological data. PMID:16836764
The RCSB PDB information portal for structural genomics. PMID:16381872
Detailed protein sequence alignment based on Spectral Similarity Score (SSS). PMID:15850477
Identification of the ligand binding sites on the molecular surface of proteins. PMID:15689509
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
E-MSD: an integrated data resource for bioinformatics. PMID:15608192
InterPro, progress and status in 2005. PMID:15608177
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. PMID:15459285
Structure determination of membrane proteins by NMR spectroscopy. PMID:15303829
Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms. PMID:15272176 -
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
PubMed citations: 413.
413 articles citing: The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds. PMID:35327963
Drug Design-Past, Present, Future. PMID:35268598
The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2. PMID:35252354
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. PMID:35049908
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind's AlphaFold2 Program Dramatically Expands the Metalloproteome. PMID:34838520
Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. PMID:34502559
Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups. PMID:34490059
At sixes and sevens: cryptic domain in the metal binding chain of the human copper transporter ATP7A. PMID:34461106
Entanglements of structure elements revealed in RNA 3D models. PMID:34432024
Ankyrin repeats in context with human population variation. PMID:34428215
Quest for Novel Preventive and Therapeutic Options Against Multidrug-Resistant Pseudomonas aeruginosa. PMID:34393689
Prediction of MoRFs based on sequence properties and convolutional neural networks. PMID:34391457
Assessing the utility of CASP14 models for molecular replacement. PMID:34387010
Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions. PMID:34345854
Development of antibacterial compounds that constrain evolutionary pathways to resistance. PMID:34279221
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences. PMID:34228733
DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data. PMID:34216059
Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review. PMID:34132259
Modelling covalent linkages in CCP4. PMID:34076587
Protein Structure Prediction: Conventional and Deep Learning Perspectives. PMID:34050498
Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach. PMID:34026848
Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA. PMID:33925823
Online biophysical predictions for SARS-CoV-2 proteins. PMID:33892639
Potential combination therapy using twenty phytochemicals from twenty plants to prevent SARS- CoV-2 infection: An in silico Approach. PMID:33842675
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. PMID:33634309
Analogue discovery of safer alternatives to HCQ and CQ drugs for SAR-CoV-2 by computational design. PMID:33535144
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. PMID:33502860
Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1. PMID:33499226
ACID: a free tool for drug repurposing using consensus inverse docking strategy. PMID:33430982
Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. PMID:33425253
N-Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides: Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents. PMID:33375766
Functional Dependency Analysis Identifies Potential Druggable Targets in Acute Myeloid Leukemia. PMID:33321907
Understanding the biological role of PqqB in Pseudomonas stutzeri using molecular dynamics simulation approach. PMID:33287678
Prediction of MoRFs in Protein Sequences with MLPs Based on Sequence Properties and Evolution Information. PMID:33267349
Shift-field refinement of macromolecular atomic models. PMID:33263325
Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach. PMID:33154404
Pfam: The protein families database in 2021. PMID:33125078
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. PMID:33028652
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. PMID:33006605
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. PMID:32879328
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age. PMID:32849618
Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. PMID:32839613
ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques. PMID:32780798
Toxin transcripts in Crotalus atrox venom and in silico structures of toxins. PMID:32774833
Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR). PMID:32755705
Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. PMID:32731448
Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. PMID:32636380
Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. PMID:32620933
Genetic variability of human angiotensin-converting enzyme 2 (hACE2) among various ethnic populations. PMID:32558308
Computational investigation on Andrographis paniculata phytochemicals to evaluate their potency against SARS-CoV-2 in comparison to known antiviral compounds in drug trials. PMID:32543978
Structure of the SARS-Unique Domain C From the Bat Coronavirus HKU4. PMID:32395093
Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. PMID:32392301
Modelling of pH-dependence to develop a strategy for stabilising mAbs at acidic steps in production. PMID:32322371
The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication. PMID:32294919
C─H⋯O hydrogen bonds in kinase-inhibitor interfaces. PMID:32271995
Structural Insights into the Mammalian Late-Stage Initiation Complexes. PMID:32268096
Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. PMID:32242052
Measuring and using information gained by observing diffraction data. PMID:32133988
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. PMID:32069281
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. PMID:32054457
Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations. PMID:32053772
Charge and hydrophobicity are key features in sequence-trained machine learning models for predicting the biophysical properties of clinical-stage antibodies. PMID:31976163
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
Facilities that make the PDB data collection more powerful. PMID:31724231
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Computational prediction of MoRFs based on protein sequences and minimax probability machine. PMID:31660849
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Synthesis and Biological Activity of a Bis-steroid-Methanocyclobutanaphthalene- dione Derivative against Ischemia/Reperfusion Injury via Calcium Channel Activation. PMID:31580254
Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). PMID:31571280
Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank. PMID:31480623
Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins. PMID:31458221
Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea. PMID:31435153
Evaluation of template-based modeling in CASP13. PMID:31407380
Stability of buried and networked salt-bridges (BNSB)in thermophilic proteins. PMID:31360001
Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review. PMID:31303975
Archiving and disseminating integrative structure models. PMID:31278630
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
I-PINE web server: an integrative probabilistic NMR assignment system for proteins. PMID:31165321
Envisioning data sharing for the biocomputing community. PMID:31065349
Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a. PMID:30950405
Molecular evolution of Pr1 proteases depicts ongoing diversification in Metarhizium spp. PMID:30923942
BLASTing away preconceptions in crystallization trials. PMID:30839293
Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PMID:30834181
Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins: A Study for Peptidyl-Prolyl cis/trans Isomerases (PPIase). PMID:30754725
Protein-protein binding supersites. PMID:30615604
Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank. PMID:30537764
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
Thermal stability of single-domain antibodies estimated by molecular dynamics simulations. PMID:30394618
High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure. PMID:30387765
Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update). PMID:30357361
The Pfam protein families database in 2019. PMID:30357350
Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer's Disease: A Computational Study. PMID:30332805
Copper mediated amyloid-β binding to Transthyretin. PMID:30213975
The calcium-binding site of human glutamate carboxypeptidase II is critical for dimerization, thermal stability, and enzymatic activity. PMID:30168215
Automatic 13C chemical shift reference correction for unassigned protein NMR spectra. PMID:30097912
SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PMID:29975698
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
Molecular nucleation mechanisms and control strategies for crystal polymorph selection. PMID:29620730
Total energy expenditure in adults aged 65 years and over measured using doubly-labelled water: international data availability and opportunities for data sharing. PMID:29580255
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
Macromolecular refinement by model morphing using non-atomic parameterizations. PMID:29533238
Primary and Higher Order Structure of the Reaction Center from the Purple Phototrophic Bacterium Blastochloris viridis: A Test for Native Mass Spectrometry. PMID:29466012
Identification of Cross Reactive Antigens of C. botulinum Types A, B, E & F by Immunoproteomic Approach. PMID:29332140
Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state. PMID:29309620
How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. PMID:29276518
3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. PMID:29244774
Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents. PMID:29186912
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12. PMID:29178137
Evaluation of the template-based modeling in CASP12. PMID:29159950
All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds. PMID:29119109
Peptidylprolyl Isomerases as In Vivo Carriers for Drugs That Target Various Intracellular Entities. PMID:28961224
Forty years of collaborative computational crystallography. PMID:28901632
PDBsum: Structural summaries of PDB entries. PMID:28875543
Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment. PMID:28828285
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. PMID:28811629
Bradyrhizobium elkanii nod regulon: insights through genomic analysis. PMID:28767122
Unique identifiers for small molecules enable rigorous labeling of their atoms. PMID:28534867
Biomolecular NMR: Past and future. PMID:28495511
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. PMID:28453649
A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. PMID:28302053
Site-based data curation based on hot spring geobiology. PMID:28253269
Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin. PMID:28235019
X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC. PMID:28045390
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures. PMID:27964945
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. PMID:27924013
A closer look into the α-helix basin. PMID:27917894
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697
Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods? PMID:27748116
Validation and correction of Zn-CysxHisy complexes. PMID:27710932
PCDDB: new developments at the Protein Circular Dichroism Data Bank. PMID:27613420
Revisiting antibody modeling assessment for CDR-H3 loop. PMID:27515703
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution. PMID:27493524
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. PMID:27475771
Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations. PMID:27334455
Landscape of protein-small ligand binding modes. PMID:27327045
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
The RING 2.0 web server for high quality residue interaction networks. PMID:27198219
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis. PMID:27107576
SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations. PMID:27077847
A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments. PMID:26978354
Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines. PMID:26960128
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize. PMID:26828478
Probabilistic validation of protein NMR chemical shift assignments. PMID:26724815
Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PMID:26642067
Database resources of the National Center for Biotechnology Information. PMID:26615191
EMDataBank unified data resource for 3DEM. PMID:26578576
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. PMID:26508754
DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data. PMID:26504146
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets. PMID:26307973
MultiSETTER: web server for multiple RNA structure comparison. PMID:26264783
Detection of trans-cis flips and peptide-plane flips in protein structures. PMID:26249342
Implication from the predicted docked interaction of sigma H and exploration of its interaction with RNA polymerase in Mycobacterium tuberculosis. PMID:26229290
The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease. PMID:26173036
Large-scale Direct Targeting for Drug Repositioning and Discovery. PMID:26155766
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. PMID:26117545
DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach. PMID:26090958
Heterozygous reelin mutations cause autosomal-dominant lateral temporal epilepsy. PMID:26046367
NMR Exchange Format: a unified and open standard for representation of NMR restraint data. PMID:26036565
HMMER web server: 2015 update. PMID:25943547
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
Binding cavities and druggability of intrinsically disordered proteins. PMID:25611056
Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of streptococcal isomerase and dehydrogenase. PMID:25605731
Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets. PMID:25574133
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. PMID:25505092
Automated nucleic acid chain tracing in real time. PMID:25485119
On the role of physics and evolution in dictating protein structure and function. PMID:25484448
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Anatomy of enzyme channels. PMID:25403510
Database resources of the National Center for Biotechnology Information. PMID:25398906
SASBDB, a repository for biological small-angle scattering data. PMID:25352555
sc-PDB: a 3D-database of ligandable binding sites--10 years on. PMID:25300483
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. PMID:25212755
PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. PMID:25190042
ProBLM web server: protein and membrane placement and orientation package. PMID:25126110
AFAL: a web service for profiling amino acids surrounding ligands in proteins. PMID:25085083
The PDB_REDO server for macromolecular structure model optimization. PMID:25075342
Signaling domain of Sonic Hedgehog as cannibalistic calcium-regulated zinc-peptidase. PMID:25033298
Systems biology in the context of big data and networks. PMID:24982882
Structural insights into SraP-mediated Staphylococcus aureus adhesion to host cells. PMID:24901708
Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns. PMID:24850495
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. PMID:24848013
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. PMID:24782522
A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PMID:24762569
Prediction and analysis of canonical EF hand loop and qualitative estimation of Ca²⁺ binding affinity. PMID:24760183
Protein-protein interaction detection: methods and analysis. PMID:24693427
Helix kinks are equally prevalent in soluble and membrane proteins. PMID:24638929
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease. PMID:24598793
Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction. PMID:24564918
Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. PMID:24493012
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Interplay between peptide bond geometrical parameters in nonglobular structural contexts. PMID:24455689
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. PMID:24423161
Motif-directed redesign of enzyme specificity. PMID:24407908
The ABCA1 domain responsible for interaction with HIV-1 Nef is conformational and not linear. PMID:24406162
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. PMID:24318998
Split green fluorescent protein as a modular binding partner for protein crystallization. PMID:24311592
PDBe: Protein Data Bank in Europe. PMID:24288376
The European Bioinformatics Institute's data resources 2014. PMID:24271396
PANADA: protein association network annotation, determination and analysis. PMID:24265686
Database resources of the National Center for Biotechnology Information. PMID:24259429
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method. PMID:24124577
Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. PMID:24121683
Unexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine-rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue. PMID:24100551
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PMID:24098102
Role of glycoside phosphorylases in mannose foraging by human gut bacteria. PMID:24043624
Protein modeling: what happened to the "protein structure gap"? PMID:24010712
How community has shaped the Protein Data Bank. PMID:24010707
Structural templates for modeling homodimers. PMID:23996787
Space constrained homology modelling: the paradigm of the RNA-dependent RNA polymerase of dengue (type II) virus. PMID:23986788
PDB@: an offline toolkit for exploration and analysis of PDB files. PMID:23982150
Reassessing buried surface areas in protein-protein complexes. PMID:23934783
Exhaustive comparison and classification of ligand-binding surfaces in proteins. PMID:23934772
An overview of tools for the validation of protein NMR structures. PMID:23877928
Discovery of novel candidate therapeutics and diagnostics based on engineered human antibody domains. PMID:23863097
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. PMID:23826885
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. PMID:23815411
Correlation spectroscopy and molecular dynamics simulations to study the structural features of proteins. PMID:23750215
Interplay of physics and evolution in the likely origin of protein biochemical function. PMID:23690621
A ligand-specific kinetic switch regulates glucocorticoid receptor trafficking and function. PMID:23687373
Modeling proteins using a super-secondary structure library and NMR chemical shift information. PMID:23685209
Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. PMID:23665222
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
ValiDichro: a website for validating and quality control of protein circular dichroism spectra. PMID:23625965
Solvated protein-DNA docking using HADDOCK. PMID:23625455
Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. PMID:23530042
Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins. PMID:23526551
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. PMID:23526422
In silico structural and functional characterization of the RSUME splice variants. PMID:23469069
Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants. PMID:23369338
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
Molecular interaction study of N1-p-fluorobenzyl-cymserine with TNF-α , p38 kinase and JNK kinase. PMID:23360257
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics. PMID:23296088
Functional diversity and pharmacological profiles of the FKBPs and their complexes with small natural ligands. PMID:23224428
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. PMID:23203986
Database resources of the National Center for Biotechnology Information. PMID:23193264
Influence of structural symmetry on protein dynamics. PMID:23189176
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. PMID:23180575
A rule-based algorithm for automatic bond type perception. PMID:23113939
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. PMID:23095257
Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. PMID:22974364
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. PMID:22962462
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. PMID:22962312
Correlation between protein sequence similarity and crystallization reagents in the biological macromolecule crystallization database. PMID:22949812
PACSY, a relational database management system for protein structure and chemical shift analysis. PMID:22903636
Alternative protein-protein interfaces are frequent exceptions. PMID:22876170
ACPYPE - AnteChamber PYthon Parser interfacE. PMID:22824207
Analysis of conformational variation in macromolecular structural models. PMID:22808083
Fungal genome resources at NCBI. PMID:22737589
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. PMID:22730453
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. PMID:22689782
DichroMatch: a website for similarity searching of circular dichroism spectra. PMID:22638573
A query integrator and manager for the query web. PMID:22531831
A frontier in the understanding of synaptic plasticity: solving the structure of the postsynaptic density. PMID:22528972
Implementing an X-ray validation pipeline for the Protein Data Bank. PMID:22505268
On the need for an international effort to capture, share and use crystallization screening data. PMID:22442216
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
PrionHome: a database of prions and other sequences relevant to prion phenomena. PMID:22363733
Composite structural motifs of binding sites for delineating biological functions of proteins. PMID:22347478
Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. PMID:22323219
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Data issues in the life sciences. PMID:22207805
Modulating protein-protein interactions with small molecules: the importance of binding hotspots. PMID:22198293
Database resources of the National Center for Biotechnology Information. PMID:22140104
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
PDBe: Protein Data Bank in Europe. PMID:22110033
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
Structural annotation of Mycobacterium tuberculosis proteome. PMID:22073123
A conserved interaction with the chromophore of fluorescent proteins. PMID:22057893
A de novo peptide hexamer with a mutable channel. PMID:22037471
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. PMID:22034521
Some B(eq) are more equivalent than others. PMID:22011466
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. PMID:21993301
Improving the prediction of disease-related variants using protein three-dimensional structure. PMID:21992054
Assessment of ligand-binding residue predictions in CASP9. PMID:21987472
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. PMID:21976737
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice. PMID:21936904
Synergistic use of plant-prokaryote comparative genomics for functional annotations. PMID:21810204
Structural mass spectrometry of proteins using hydroxyl radical based protein footprinting. PMID:21770468
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. PMID:21646342
The eisosome core is composed of BAR domain proteins. PMID:21593205
Graphical representation and mathematical characterization of protein sequences and applications to viral proteins. PMID:21570664
Accuracy of functional surfaces on comparatively modeled protein structures. PMID:21541664
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. PMID:21521828
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
Data processing and analysis with the autoPROC toolbox. PMID:21460447
Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm. PMID:21406389
Crystal structure of Toxoplasma gondii porphobilinogen synthase: insights on octameric structure and porphobilinogen formation. PMID:21383008
Common structural traits for cystine knot domain of the TGFβ superfamily of proteins and three-fingered ectodomain of their cellular receptors. PMID:21369710
ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structures at different distance threshold. PMID:21346863
Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus. PMID:21280117
PSD-95 alters microtubule dynamics via an association with EB3. PMID:21248129
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. PMID:21246630
An Integrated Database for Complex Protein Structure Modeling. PMID:21151784
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities. PMID:21123384
Database resources of the National Center for Biotechnology Information. PMID:21097890
BISC: binary subcomplexes in proteins database. PMID:21081561
A computational study of CYP3A4 mediated drug interaction profiles for anti-HIV drugs. PMID:21080015
A series of PDB related databases for everyday needs. PMID:21071423
PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata. PMID:21071417
Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage. PMID:21062824
Biased retrieval of chemical series in receptor-based virtual screening. PMID:21053053
Computer-aided drug design platform using PyMOL. PMID:21053052
PDBe: Protein Data Bank in Europe. PMID:21045060
GlycomeDB--a unified database for carbohydrate structures. PMID:21045056
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces. PMID:20981266
3did: identification and classification of domain-based interactions of known three-dimensional structure. PMID:20965963
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. PMID:20952398
BSDB: the biomolecule stretching database. PMID:20929872
Structural characterization of naturally occurring RNA single mismatches. PMID:20876693
Sustainable digital infrastructure. Although databases and other online resources have become a central tool for biological research, their long-term support and maintenance is far from secure. PMID:20847740
Template-based protein structure modeling. PMID:20835794
A protein sequence meta-functional signature for calcium binding residue prediction. PMID:20824111
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. PMID:20798081
2Struc: the secondary structure server. PMID:20739308
Straightforward and complete deposition of NMR data to the PDBe. PMID:20680401
Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach. PMID:20634983
n-->pi* interactions in proteins. PMID:20622857
Validation of archived chemical shifts through atomic coordinates. PMID:20602353
Molecular aspects of cyclophilins mediating therapeutic actions of their ligands. PMID:20602248
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. PMID:20550657
A multilevel data integration resource for breast cancer study. PMID:20525248
NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints. PMID:20513646
Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. PMID:20505002
Application of protein engineering to enhance crystallizability and improve crystal properties. PMID:20445236
The Scottish Structural Proteomics Facility: targets, methods and outputs. PMID:20419351
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
Small Molecule Subgraph Detector (SMSD) toolkit. PMID:20298518
Characterization of protein secondary structure from NMR chemical shifts. PMID:20160946
HDAPD: a web tool for searching the disease-associated protein structures. PMID:20158919
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. PMID:20157485
Practical application of bioinformatics by the multidisciplinary VIZIER consortium. PMID:20153379
Automated detection of conformational epitopes using phage display Peptide sequences. PMID:20140073
Evolutionary trace annotation of protein function in the structural proteome. PMID:20036248
Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure. PMID:20015380
The European Bioinformatics Institute's data resources. PMID:19934258
Evolution by leaps: gene duplication in bacteria. PMID:19930658
Database resources of the National Center for Biotechnology Information. PMID:19910364
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
Why hypothetical protein KPN00728 of Klebsiella pneumoniae should be classified as chain C of succinate dehydrogenase? PMID:19859792
PDBe: Protein Data Bank in Europe. PMID:19858099
The role of medical structural genomics in discovering new drugs for infectious diseases. PMID:19855826
The IntAct molecular interaction database in 2010. PMID:19850723
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
The continuity of protein structure space is an intrinsic property of proteins. PMID:19805219
The interwinding nature of protein-protein interfaces and its implication for protein complex formation. PMID:19789269
Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition. PMID:19776130
Computational modeling of novel inhibitors targeting the Akt pleckstrin homology domain. PMID:19734051
Assessment of ligand binding residue predictions in CASP8. PMID:19714771
A guide to the Proteomics Identifications Database proteomics data repository. PMID:19662629
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction. PMID:19615046
Benefits of structural genomics for drug discovery research. PMID:19594422
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
Water polygons in high-resolution protein crystal structures. PMID:19551896
Effective knowledge-based potentials. PMID:19530247
SARA: a server for function annotation of RNA structures. PMID:19483098
Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition. PMID:19413567
GeNMR: a web server for rapid NMR-based protein structure determination. PMID:19406927
The role of entropy and polarity in intermolecular contacts in protein crystals. PMID:19390155
Relationship between chemical shift value and accessible surface area for all amino acid atoms. PMID:19341463
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. PMID:19219566
Structural genomics is the largest contributor of novel structural leverage. PMID:19194785
VASCo: computation and visualization of annotated protein surface contacts. PMID:19166624
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
Data deposition and annotation at the worldwide protein data bank. PMID:19082769
The Protein Model Portal. PMID:19037750
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. PMID:18989261
3did Update: domain-domain and peptide-mediated interactions of known 3D structure. PMID:18953040
Database resources of the National Center for Biotechnology Information. PMID:18940862
InterPro: the integrative protein signature database. PMID:18940856
The SWISS-MODEL Repository and associated resources. PMID:18931379
Prediction of TF target sites based on atomistic models of protein-DNA complexes. PMID:18922190
TMFunction: database for functional residues in membrane proteins. PMID:18842639
SuperSite: dictionary of metabolite and drug binding sites in proteins. PMID:18842629
Cell cycle kinases predicted from conserved biophysical properties. PMID:18704950
A protein-DNA docking benchmark. PMID:18583363
K2D2: estimation of protein secondary structure from circular dichroism spectra. PMID:18477405
Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses. PMID:18469082
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. PMID:18463137
TarO: a target optimisation system for structural biology. PMID:18385152
Hysteretic and graded responses in bacterial two-component signal transduction. PMID:18363790
Structural inference of native and partially folded RNA by high-throughput contact mapping. PMID:18322008
Alternative splicing and protein structure evolution. PMID:18055499
Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ. PMID:18046455
Database resources of the National Center for Biotechnology Information. PMID:18045790
DIMA 2.0--predicted and known domain interactions. PMID:17999995
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. PMID:17984082
The Molecule Pages database. PMID:17965093
High-resolution structure prediction and the crystallographic phase problem. PMID:17934447
ProSAS: a database for analyzing alternative splicing in the context of protein structures. PMID:17933774
AutoPSI: a database for automatic structural classification of protein sequences and structures. PMID:17932066
ChEBI: a database and ontology for chemical entities of biological interest. PMID:17932057
A global analysis of NMR distance constraints from the PDB. PMID:17922259
coliSNP database server mapping nsSNPs on protein structures. PMID:17921498
Sharing and reusing gene expression profiling data in neuroscience. PMID:17917127
PPT-DB: the protein property prediction and testing database. PMID:17916570
Crystallization and diffraction data of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase: a cofactor-free oxygenase of the alpha/beta-hydrolase family. PMID:17565175
FastContact: a free energy scoring tool for protein-protein complex structures. PMID:17537824
A cheminformatic toolkit for mining biomedical knowledge. PMID:17385012 -
Protein Data Bank: the single global archive for 3D macromolecular structure data
PubMed citations: 208.
208 articles citing: Protein Data Bank: the single global archive for 3D macromolecular structure data
AlphaFold predicts the most complex protein knot and composite protein knots. PMID:35900026
Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. PMID:35887033
CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome. PMID:35883523
Repair of Iron Center Proteins-A Different Class of Hemerythrin-like Proteins. PMID:35807291
Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation. PMID:35806248
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
The zinc proteome of SARS-CoV-2. PMID:35767875
Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. PMID:35758198
Epitope identification of SARS-CoV-2 structural proteins using in silico approaches to obtain a conserved rational immunogenic peptide. PMID:35721890
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV. PMID:35664235
Predicting epitopes for vaccine development using bioinformatics tools. PMID:35647486
Complementarity of the residue-level protein function and structure predictions in human proteins. PMID:35615015
Large-Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families. PMID:35608365
rna-tools.online: a Swiss army knife for RNA 3D structure modeling workflow. PMID:35580057
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. PMID:35566372
Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters. PMID:35563448
Validation analysis of EMDB entries. PMID:35503203
Genome-Wide Analysis of Invertase Gene Family, and Expression Profiling under Abiotic Stress Conditions in Potato. PMID:35453738
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. PMID:35447030
Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches. PMID:35356248
BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network. PMID:35328384
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PMID:35294442
An Integrative Pharmacology Model for Decoding the Underlying Therapeutic Mechanisms of Ermiao Powder for Rheumatoid Arthritis. PMID:35281924
Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. PMID:35264796
Enhancing DNT Detection by a Bacterial Bioreporter: Directed Evolution of the Transcriptional Activator YhaJ. PMID:35237579
The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes. PMID:35212369
Localpdb- a Python package to manage protein structures and their annotations. PMID:35199148
Identification of Corosolic and Oleanolic Acids as Molecules Antagonizing the Human RORγT Nuclear Receptor Using the Calculated Fingerprints of the Molecular Similarity. PMID:35163824
Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. PMID:35154362
Modelling of the dynamic polarizability of macromolecules for single-molecule optical biosensing. PMID:35132077
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Linking protein structural and functional change to mutation using amino acid networks. PMID:35061689
Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. PMID:35061391
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. PMID:34930115
Random sampling of the Protein Data Bank: RaSPDB. PMID:34921198
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Machine learning to estimate the local quality of protein crystal structures. PMID:34880321
New system for archiving integrative structures. PMID:34866606
Fifty years of Protein Data Bank in the Journal of Biochemistry. PMID:34865074
The possible mechanism of Hippophae fructus oil applied in tympanic membrane repair identified based on network pharmacology and molecular docking. PMID:34859918
Fractional-Order Susceptible-Infected Model: Definition and Applications to the Study of COVID-19 Main Protease. PMID:34849076
Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. PMID:34804551
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. PMID:34791371
Lipid Anchoring Improves Lubrication and Wear Resistance of the Collagen I Matrix. PMID:34788036
PDBsum extras: SARS-CoV-2 and AlphaFold models. PMID:34779073
Building Structural Models of a Whole Mycoplasma Cell. PMID:34774566
PDBe-KB: collaboratively defining the biological context of structural data. PMID:34755867
Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. PMID:34745807
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
The importance of adherence to international standards for depositing open data in public repositories. PMID:34727971
Diversification of Ferredoxins across Living Organisms. PMID:34698119
Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. PMID:34689168
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
AI revolutions in biology: The joys and perils of AlphaFold. PMID:34668287
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease. PMID:34628220
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
Molecular Docking and Simulation Studies of Antidiabetic Agents Devised from Hypoglycemic Polypeptide-P of Momordica charantia. PMID:34589547
Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. PMID:34580920
Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. PMID:34578452
Midkine promotes glioblastoma progression via PI3K-Akt signaling. PMID:34556138
Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure. PMID:34541552
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. PMID:34506132
Identification of potential therapeutic targets and mechanisms of COVID-19 through network analysis and screening of chemicals and herbal ingredients. PMID:34505138
Accelerating antibiotic discovery through artificial intelligence. PMID:34504303
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed. PMID:34477506
New restraints and validation approaches for nucleic acid structures in PDB-REDO. PMID:34473084
Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. PMID:34458830
Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures. PMID:34445259
Ankyrin repeats in context with human population variation. PMID:34428215
A Comparative Study of Machine Learning Methods for Persistence Diagrams. PMID:34396089
Continuous Automated Model EvaluatiOn (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods. PMID:34387007
Network Pharmacology and Experimental Evidence: PI3K/AKT Signaling Pathway is Involved in the Antidepressive Roles of Chaihu Shugan San. PMID:34385814
Online bioinformatics teaching practice: Comparison of popular docking programs using SARS-CoV-2 spike RBD-ACE2 complex as a benchmark. PMID:34369638
Assessing the binding properties of CASP14 targets and models. PMID:34368994
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Highly accurate protein structure prediction with AlphaFold. PMID:34265844
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785
Understanding the structural details of APOBEC3-DNA interactions using graph-based representations. PMID:34235473
The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins. PMID:34206634
EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization. PMID:34206006
Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study. PMID:34109214
PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data. PMID:34081107
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. PMID:34021280
Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis. PMID:33995335
Mechanism of MRX inhibition by Rif2 at telomeres. PMID:33980827
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
From integrative structural biology to cell biology. PMID:33957123
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. PMID:33956157
Validation by Molecular Dynamics of the Major Components of Sugarcane Vinasse, On a Surface of Calcium Carbonate (Calcite). PMID:33919518
Web resources facilitate drug discovery in treatment of COVID-19. PMID:33892145
Potent sialic acid inhibitors that target influenza A virus hemagglutinin. PMID:33883588
Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing. PMID:33877262
Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. PMID:33823127
Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies. PMID:33810118
Characterization of the Bubblegum acyl-CoA synthetase of Microchloropsis gaditana. PMID:33793914
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
Sequence Alignment Using Machine Learning for Accurate Template-based Protein Structure Prediction. PMID:33659566
Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations. PMID:33658550
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. PMID:33559613
Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. PMID:33550681
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. PMID:33542514
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. PMID:33496579
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail. PMID:33477938
Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems. PMID:33452479
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. PMID:33404525
A comparison between internal protein nanoenvironments of α-helices and β-sheets. PMID:33378364
N-Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides: Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents. PMID:33375766
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs. PMID:33300028
Real-time structural motif searching in proteins using an inverted index strategy. PMID:33284792
Histone tails as signaling antennas of chromatin. PMID:33279866
High-performance macromolecular data delivery and visualization for the web. PMID:33263322
Arginine off-kilter: guanidinium is not as planar as restraints denote. PMID:33263321
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
Experimental phasing with vanadium and application to nucleotide-binding membrane proteins. PMID:33209320
BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics. PMID:33206646
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
De Novo VPS4A Mutations Cause Multisystem Disease with Abnormal Neurodevelopment. PMID:33186545
Structural basis of acquired resistance to selpercatinib and pralsetinib mediated by non-gatekeeper RET mutations. PMID:33161056
DescribePROT: database of amino acid-level protein structure and function predictions. PMID:33119734
Automated and optimally FRET-assisted structural modeling. PMID:33106483
Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19. PMID:33101604
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PMID:33075050
Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog. PMID:32988830
Diversity and evolution of B-family DNA polymerases. PMID:32976577
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. PMID:32857966
Sequence alignment generation using intermediate sequence search for homology modeling. PMID:32802276
A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. PMID:32776019
The data universe of structural biology. PMID:32695409
Real time structural search of the Protein Data Bank. PMID:32639954
Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. PMID:32637803
Probabilistic identification of saccharide moieties in biomolecules and their protein complexes. PMID:32620933
Topological analysis of SARS CoV-2 main protease. PMID:32611087
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
Ultrastructural Location and Interactions of the Immunoglobulin Receptor Binding Sequence within Fibrillar Type I Collagen. PMID:32545195
The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. PMID:32507889
Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins. PMID:32502383
The Architectural Dynamics of the Bacterial Flagellar Motor Switch. PMID:32486003
TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. PMID:32479639
ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam. PMID:32381789
Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space. PMID:32353118
An In Silico Target Fishing Approach to Identify Novel Ochratoxin A Hydrolyzing Enzyme. PMID:32316122
Why does oxamniquine kill Schistosoma mansoni and not S. haematobium and S. japonicum? PMID:32315953
Structural Phylogenetics with Confidence. PMID:32302382
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. PMID:32297936
Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. PMID:32231015
Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. PMID:32144738
What are the current limits on determination of protonation state using neutron macromolecular crystallography? PMID:32093835
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
Big data science at AMED-BINDS. PMID:32030637
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations. PMID:32026396
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
BioMagResBank (BMRB) as a Resource for Structural Biology. PMID:32006287
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency. PMID:32005745
Evolving data standards for cryo-EM structures. PMID:32002441
Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations. PMID:31996730
The current understanding of KRAS protein structure and dynamics. PMID:31988705
Propensities of Amino Acid Pairings in Secondary Structure of Globular Proteins. PMID:31933010
Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. PMID:31819058
Molecular replacement using structure predictions from databases. PMID:31793899
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Using Structural Analysis In Silico to Assess the Impact of Missense Variants in MEN1. PMID:31737856
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. PMID:31724711
Facilities that make the PDB data collection more powerful. PMID:31724231
Ensembl 2020. PMID:31691826
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Norine: update of the nonribosomal peptide resource. PMID:31691799
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration. PMID:31680154
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data. PMID:31614716
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
SASBDB: Towards an automatically curated and validated repository for biological scattering data. PMID:31576635
Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). PMID:31571280
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. PMID:31506435
Understanding protein multifunctionality: from short linear motifs to cellular functions. PMID:31432235
Origins of peptidases. PMID:31377195
3D-structured supports create complete data sets for electron crystallography. PMID:31346178
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. PMID:31263870
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. PMID:31114897
Yvis: antibody high-density alignment visualization and analysis platform with an integrated database. PMID:31106372
Design guidelines for an electron diffractometer for structural chemistry and structural biology. PMID:31063148
Modeling of Protein⁻Protein Interactions in Cytokinin Signal Transduction. PMID:31035389
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
Building and rebuilding N-glycans in protein structure models. PMID:30988258
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
Finding enzyme cofactors in Protein Data Bank. PMID:30759194
pdb-tools: a swiss army knife for molecular structures. PMID:30705752
Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. PMID:30694665
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175
NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. PMID:30580387
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411 -
Validation of Structures in the Protein Data Bank
PubMed citations: 90.
90 articles citing: Validation of Structures in the Protein Data Bank
A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. PMID:35838364
Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis. PMID:35829618
A network pharmacology approach to explore and validate the potential targets of ginsenoside on osteoporosis. PMID:35791093
Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. PMID:35631392
Three-dimensional Structure Databases of Biological Macromolecules. PMID:35507259
Crystal structure of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (hROR1). PMID:35506763
Validation analysis of EMDB entries. PMID:35503203
Modeling and dynamical analysis of the full-length structure of factor XII with zinc. PMID:35469101
Investigating the Effects of Amino Acid Variations in Human Menin. PMID:35268848
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase. PMID:35018940
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. PMID:34819324
Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells. PMID:34696326
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles. PMID:34542291
Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). PMID:34506758
Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. PMID:34506566
Structural and Biochemical Characterization of the Flavin-Dependent Siderophore-Interacting Protein from Acinetobacter baumannii. PMID:34308084
Performance of Web tools for predicting changes in protein stability caused by mutations. PMID:34225665
Design, Synthesis, In Silico and In Vitro Studies for New Nitric Oxide-Releasing Indomethacin Derivatives with 1,3,4-oxadiazole-2-thiol Scaffold. PMID:34209248
Structure of Nanobody Nb23. PMID:34207949
Structural basis for the stereospecific inhibition of the dual proline/hydroxyproline catabolic enzyme ALDH4A1 by trans-4-hydroxy-L-proline. PMID:34048122
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
From integrative structural biology to cell biology. PMID:33957123
Structural genomics and the Protein Data Bank. PMID:33957120
Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments. PMID:33950676
The Protein Data Bank Archive. PMID:33950382
Single-Molecule FRET of Membrane Transport Proteins. PMID:33945656
Deciphering the Relationship Between Cycloheximides Structures and Their Different Biological Activities. PMID:33897655
An RNA-centric historical narrative around the Protein Data Bank. PMID:33744291
Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. PMID:33744287
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. PMID:33603257
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. PMID:33542514
Identification of potential inhibitors of Zika virus NS5 RNA-dependent RNA polymerase through virtual screening and molecular dynamic simulations. PMID:33424251
A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria. PMID:33384667
A method for validating the accuracy of NMR protein structures. PMID:33339822
Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains. PMID:33334883
Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-γ-semialdehyde dehydrogenase active site of bifunctional proline utilization A. PMID:33333077
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1. PMID:33109600
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design. PMID:33108589
Structure of the Complex of an Iminopyridinedione Protein Tyrosine Phosphatase 4A3 Phosphatase Inhibitor with Human Serum Albumin. PMID:32978326
High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. PMID:32973265
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
A chemical interpretation of protein electron density maps in the worldwide protein data bank. PMID:32785279
Membrane Chemistry Tunes the Structure of a Peptide Transporter. PMID:32744783
Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy. PMID:32743572
Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. PMID:32723870
Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1. PMID:32717224
High-resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6. PMID:32654405
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
Structure and function of a flavin-dependent S-monooxygenase from garlic (Allium sativum). PMID:32527723
Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma. PMID:32469516
Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex. PMID:32404365
On the evolution of the quality of macromolecular models in the PDB. PMID:32311227
Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy. PMID:32231015
NMDA receptor channel gating control by the pre-M1 helix. PMID:32221541
Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate. PMID:32159324
Big data science at AMED-BINDS. PMID:32030637
Evolving data standards for cryo-EM structures. PMID:32002441
Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. PMID:31968260
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. PMID:31390767
Archiving and disseminating integrative structure models. PMID:31278630
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. PMID:31263870
VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes. PMID:31073605
Anticipating innovations in structural biology. PMID:30912485
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Synthesis, Biological Evaluation and Docking Studies of Benzoxazoles Derived from Thymoquinone. PMID:30545123
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro. PMID:30499668
Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way. PMID:30425800
Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. PMID:30416256
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae. PMID:30279312
Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3. PMID:30089812
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. PMID:29968672
Real-space refinement in PHENIX for cryo-EM and crystallography. PMID:29872004
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Validation of ligands in macromolecular structures determined by X-ray crystallography. PMID:29533230
Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. PMID:29508463 -
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
PubMed citations: 62.
62 articles citing: OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
Three-dimensional Structure Databases of Biological Macromolecules. PMID:35507259
Validation analysis of EMDB entries. PMID:35503203
Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. PMID:35314715
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Adaptation to genome decay in the structure of the smallest eukaryotic ribosome. PMID:35105900
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
New system for archiving integrative structures. PMID:34866606
Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaiiO6-methylguanine-DNA methyltransferase. PMID:34866599
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. PMID:34819324
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
Modelling covalent linkages in CCP4. PMID:34076587
Machine learning enabled identification of potential SARS-CoV-2 3CLpro inhibitors based on fixed molecular fingerprints and Graph-CNN neural representations. PMID:34052441
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. PMID:33961840
From integrative structural biology to cell biology. PMID:33957123
The Protein Data Bank Archive. PMID:33950382
An RNA-centric historical narrative around the Protein Data Bank. PMID:33744291
Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. PMID:33744287
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
Real-time structural motif searching in proteins using an inverted index strategy. PMID:33284792
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity. PMID:33060678
Iris: Interactive all-in-one graphical validation of 3D protein model iterations. PMID:32964594
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
A chemical interpretation of protein electron density maps in the worldwide protein data bank. PMID:32785279
The data universe of structural biology. PMID:32695409
A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. PMID:32592631
BioMagResBank (BMRB) as a Resource for Structural Biology. PMID:32006287
Evolving data standards for cryo-EM structures. PMID:32002441
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. PMID:31750992
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
SASBDB: Towards an automatically curated and validated repository for biological scattering data. PMID:31576635
Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? PMID:31576212
Archiving and disseminating integrative structure models. PMID:31278630
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. PMID:31257108
Principles for Integrative Structural Biology Studies. PMID:31150619
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
Building and rebuilding N-glycans in protein structure models. PMID:30988258
Anticipating innovations in structural biology. PMID:30912485
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
New tools for the analysis and validation of cryo-EM maps and atomic models. PMID:30198894
Making glycoproteins a little bit sweeter with PDB-REDO. PMID:30084395
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Biocuration: Distilling data into knowledge. PMID:29659566
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Validation of Structures in the Protein Data Bank. PMID:29174494
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
The science is in the data. PMID:29123672
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. PMID:28665339
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive. PMID:28216043 -
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
PubMed citations: 61.
61 articles citing: The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents. PMID:35720115
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. PMID:35554554
Updated restraint dictionaries for carbohydrates in the pyranose form. PMID:35362468
Adding hydrogen atoms to molecular models via fragment superimposition. PMID:35351165
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
New system for archiving integrative structures. PMID:34866606
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases. PMID:34361017
The missing link: covalent linkages in structural models. PMID:34076588
Modelling covalent linkages in CCP4. PMID:34076587
Additive CHARMM36 Force Field for Nonstandard Amino Acids. PMID:34009984
Debio-0932, a second generation oral Hsp90 inhibitor, induces apoptosis in MCF-7 and MDA-MB-231 cell lines. PMID:33999319
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
The Protein Data Bank Archive. PMID:33950382
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds. PMID:33672700
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. PMID:33624202
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
Nucleotide-binding sites can enhance N-acylation of nearby protein lysine residues. PMID:33219268
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer. PMID:33093930
Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. PMID:32759758
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
Diffuse X-ray scattering from correlated motions in a protein crystal. PMID:32152274
Hierarchical-Clustering, Scaffold-Mining Exercises and Dynamics Simulations for Effectual Inhibitors Against Lipid-A Biosynthesis of Helicobacter pylori. PMID:31719913
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. PMID:31263870
Finding enzyme cofactors in Protein Data Bank. PMID:30759194
Iron-sulfur clusters have no right angles. PMID:30644841
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Making glycoproteins a little bit sweeter with PDB-REDO. PMID:30084395
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Structural analysis of glycoproteins: building N-linked glycans with Coot. PMID:29652253
A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity. PMID:29602904
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Validation of Structures in the Protein Data Bank. PMID:29174494
MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PMID:28574982
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. PMID:28497616
Tools for ligand validation in Coot. PMID:28291755
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Strategies for carbohydrate model building, refinement and validation. PMID:28177313
An editor for the generation and customization of geometry restraints. PMID:28177308
Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes. PMID:28177305
Classification of ligand molecules in PDB with graph match-based structural superposition. PMID:28012138
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
FreeSASA: An open source C library for solvent accessible surface area calculations. PMID:26973785
First structure of full-length mammalian phenylalanine hydroxylase reveals the architecture of an autoinhibited tetramer. PMID:26884182
Smiles2Monomers: a link between chemical and biological structures for polymers. PMID:26715946
Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. PMID:26527733
KLIFS: a structural kinase-ligand interaction database. PMID:26496949
NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. PMID:26123317
Many InChIs and quite some feat. PMID:26081259 -
The Protein Data Bank archive as an open data resource
PubMed citations: 48.
48 articles citing: The Protein Data Bank archive as an open data resource
Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. PMID:35408761
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. PMID:33833657
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PMID:33075050
An integrated exploration of pharmacological potencies of Bischofia javanica (Blume) leaves through experimental and computational modeling. PMID:32984603
A Novel Network Pharmacology Strategy to Decode Metabolic Biomarkers and Targets Interactions for Depression. PMID:32760300
A Multiscale Model to Predict Neuronal Cell Deformation with Varying Extracellular Matrix Stiffness and Topography. PMID:32426060
Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations. PMID:31951485
The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years. PMID:31768399
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease. PMID:31360335
D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. PMID:31057345
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
Brazilian malaria molecular targets (BraMMT): selected receptors for virtual high-throughput screening experiments. PMID:30810604
A Network Pharmacology-Based Approach to Investigate the Novel TCM Formula against Huntington's Disease and Validated by Support Vector Machine Model. PMID:30643534
Homology-based loop modeling yields more complete crystallographic protein structures. PMID:30224962
Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors. PMID:30112206
Marine Bacterial Compounds Evaluated by In Silico Studies as Antipsychotic Drugs Against Schizophrenia. PMID:30019186
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database. PMID:29777317
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors. PMID:29651716
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells. PMID:29510740
Synthesis, SAR, and Docking Studies Disclose 2-Arylfuran-1,4-naphthoquinones as In Vitro Antiplasmodial Hits. PMID:29225629
CryoEM-based hybrid modeling approaches for structure determination. PMID:29107896
All-atom molecular dynamics comparison of disease-associated zinc fingers. PMID:28814200
Statin and rottlerin small-molecule inhibitors restrict colon cancer progression and metastasis via MACC1. PMID:28570591
Characterizing the Hot Spots Involved in RON-MSPβ Complex Formation Using In Silico Alanine Scanning Mutagenesis and Molecular Dynamics Simulation. PMID:28507948
SEL120-34A is a novel CDK8 inhibitor active in AML cells with high levels of serine phosphorylation of STAT1 and STAT5 transactivation domains. PMID:28422713
Micro-Environmental Signature of The Interactions between Druggable Target Protein, Dipeptidyl Peptidase-IV, and Anti-Diabetic Drugs. PMID:28367418
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
A broad pH range and processive chitinase from a metagenome library. PMID:28076454
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads. PMID:27977135
Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets. PMID:27862010
Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. PMID:27455965
Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains. PMID:27345490
Data publication with the structural biology data grid supports live analysis. PMID:26947396
TRPC6 G757D Loss-of-Function Mutation Associates with FSGS. PMID:26892346
SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level. PMID:26819632
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. PMID:26582925
Comprehensive assessment of cancer missense mutation clustering in protein structures. PMID:26392535
Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers. PMID:26257829
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Data to knowledge: how to get meaning from your result. PMID:25610627
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. PMID:25392418 -
The Protein Data Bank at 40: reflecting on the past to prepare for the future
PubMed citations: 45.
45 articles citing: The Protein Data Bank at 40: reflecting on the past to prepare for the future
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
In vitro characterization of a small molecule PD-1 inhibitor that targets the PD-l/PD-L1 interaction. PMID:34996924
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles. PMID:34242248
Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. PMID:33961840
The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics. PMID:33803759
DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands. PMID:33216893
Role of the Fractalkine Receptor in CNS Autoimmune Inflammation: New Approach Utilizing a Mouse Model Expressing the Human CX3CR1I249/M280 Variant. PMID:30386211
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Uniform resolution of compact identifiers for biomedical data. PMID:29737976
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization. PMID:29295714
Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. PMID:28949136
Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures. PMID:28933304
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China<sup/> PMID:28235641
Computational methods in drug discovery. PMID:28144341
Chemical Probes and Engineered Constructs Reveal a Detailed Unfolding Mechanism for a Solvent-Free Multidomain Protein. PMID:27959526
Structural biology in antiviral drug discovery. PMID:27611878
Databases and Archiving for CryoEM. PMID:27572735
Oxygen additions in serial femtosecond crystallographic protein structures. PMID:27438534
Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase. PMID:27325739
Computing stoichiometric molecular composition from crystal structures. PMID:26089747
Protein Crystallography in Vaccine Research and Development. PMID:26068237
Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. PMID:25502373
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
Covering complete proteomes with X-ray structures: a current snapshot. PMID:25372670
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Prediction of RNA binding residues: an extensive analysis based on structure and function to select the best predictor. PMID:24658593
Celiac anti-type 2 transglutaminase antibodies induce phosphoproteome modification in intestinal epithelial Caco-2 cells. PMID:24391952
Reaction trajectory revealed by a joint analysis of protein data bank. PMID:24244274
How community has shaped the Protein Data Bank. PMID:24010707
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PMID:23990764
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences. PMID:23815227
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. PMID:23788679
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. PMID:23728592
TiPs: a database of therapeutic targets in pathogens and associated tools. PMID:23698860
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study. PMID:23575112
A combined bioinformatics and chemoinformatics approach for developing asymmetric bivalent AMPA receptor positive allosteric modulators as neuroprotective agents. PMID:23281122
Structures of a γ-aminobutyrate (GABA) transaminase from the s-triazine-degrading organism Arthrobacter aurescens TC1 in complex with PLP and with its external aldimine PLP-GABA adduct. PMID:23027742
The future of the Protein Data Bank. PMID:23023942
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844 -
The future of the Protein Data Bank
PubMed citations: 28.
28 articles citing: The future of the Protein Data Bank
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
Structure-Based Virtual Screening: From Classical to Artificial Intelligence. PMID:32411671
ECOD: identification of distant homology among multidomain and transmembrane domain proteins. PMID:31226926
Overview of the structure-based non-genomic effects of the nuclear receptor RXRα. PMID:30093910
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets. PMID:28064377
Three dimensional electron microscopy and in silico tools for macromolecular structure determination. PMID:27092033
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. PMID:26980515
Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. PMID:26793205
EMDataBank unified data resource for 3DEM. PMID:26578576
Structure-based drug design studies of the interactions of ent-kaurane diterpenes derived from Wedelia paludosa with the Plasmodium falciparum sarco/endoplasmic reticulum Ca²⁺-ATPase PfATP6. PMID:25946251
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. PMID:25627244
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
The Protein Data Bank archive as an open data resource. PMID:25062767
The evolution of enzyme function in the isomerases. PMID:25000289
Redundancy-weighting for better inference of protein structural features. PMID:24771517
A novel approach to represent and compare RNA secondary structures. PMID:24753415
Dependence of protein crystal stability on residue charge states and ion content of crystal solvent. PMID:24507608
X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. PMID:24504120
RepeatsDB: a database of tandem repeat protein structures. PMID:24311564
PDBe: Protein Data Bank in Europe. PMID:24288376
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Modelling three-dimensional protein structures for applications in drug design. PMID:24216321
Crystallographic model validation: from diagnosis to healing. PMID:24064406
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
The Protein Model Portal--a comprehensive resource for protein structure and model information. PMID:23624946
Structure of Vibrio cholerae ribosome hibernation promoting factor. PMID:23519794 -
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
PubMed citations: 27.
27 articles citing: Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
Merging NMR Data and Computation Facilitates Data-Centered Research. PMID:35111815
Simplified quality assessment for small-molecule ligands in the Protein Data Bank. PMID:35026162
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. PMID:34237886
Nanoscape, a data-driven 3D real-time interactive virtual cell environment. PMID:34191720
Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. PMID:33984281
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. PMID:33978738
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank. PMID:33657417
Membrane Proteocomplexome of Campylobacter jejuni Using 2-D Blue Native/SDS-PAGE Combined to Bioinformatics Analysis. PMID:33329413
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
Big data science at AMED-BINDS. PMID:32030637
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Inverse pharmacology: Approaches and tools for introducing druggability into engineered proteins. PMID:31494210
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). PMID:30988261
Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. PMID:30945220
Finding enzyme cofactors in Protein Data Bank. PMID:30759194
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. PMID:30595456
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. PMID:30532050
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. PMID:30357411
Protein Data Bank: the single global archive for 3D macromolecular structure data. PMID:30357364
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736 -
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
PubMed citations: 24.
24 articles citing: Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
Mechanisms of Action of Semen Ziziphi spinosae in the Treatment of Tourette Syndrome. PMID:35875687
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. PMID:35381009
Submission of structural biology data for review purposes. PMID:34866604
Submission of structural biology data for review purposes. PMID:34866597
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
Modelling covalent linkages in CCP4. PMID:34076587
Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. PMID:33961840
The Protein Data Bank Archive. PMID:33950382
ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. PMID:33833657
ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. PMID:33822884
Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. PMID:33744282
IceBear: an intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition. PMID:33559605
TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows. PMID:33404524
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive. PMID:33186584
PDB-tools web: A user-friendly interface for the manipulation of PDB files. PMID:33111403
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PMID:33075050
Local and global analysis of macromolecular atomic displacement parameters. PMID:33021494
Gold Standard for macromolecular crystallography diffraction data. PMID:32939270
RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study. PMID:32939013
The data universe of structural biology. PMID:32695409
Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. PMID:32637961
Ten quick tips for homology modeling of high-resolution protein 3D structures. PMID:32240155
Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix. PMID:32093832
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. PMID:31588918 -
The archiving and dissemination of biological structure data
PubMed citations: 18.
18 articles citing: The archiving and dissemination of biological structure data
Computational Resources for the Interpretation of Variations in Cancer. PMID:35230689
Synthesis of Anti-Inflammatory Spirostene-Pyrazole Conjugates by a Consecutive Multicomponent Reaction of Diosgenin with Oxalyl Chloride, Arylalkynes and Hydrazines or Hydrazones. PMID:35011399
The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. PMID:34237886
Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. PMID:33950392
SynPharm and the guide to pharmacology database: A toolset for conferring drug control on engineered proteins. PMID:33047381
Inverse pharmacology: Approaches and tools for introducing druggability into engineered proteins. PMID:31494210
Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. PMID:30409785
A call for public archives for biological image data. PMID:30377375
COSMIC: the Catalogue Of Somatic Mutations In Cancer. PMID:30371878
COSMIC-3D provides structural perspectives on cancer genetics for drug discovery. PMID:30158682
SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. PMID:30087931
Where is crystallography going? PMID:29533241
R3D-BLAST2: an improved search tool for similar RNA 3D substructures. PMID:29297283
Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. PMID:29258839
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
Data archiving and availability in an era of open science. PMID:28250935
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697 -
How community has shaped the Protein Data Bank
PubMed citations: 13.
13 articles citing: How community has shaped the Protein Data Bank
Involvement of GABAA Receptors in the Anxiolytic-Like Effect of Hydroxycitronellal. PMID:34222487
Structural genomics and the Protein Data Bank. PMID:33957120
Molecular interaction analysis of Sulawesi propolis compounds with SARS-CoV-2 main protease as preliminary study for COVID-19 drug discovery. PMID:33223766
Automated and optimally FRET-assisted structural modeling. PMID:33106483
Validation of ligands in macromolecular structures determined by X-ray crystallography. PMID:29533230
Improving virtual screening of G protein-coupled receptors via ligand-directed modeling. PMID:29131821
New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. PMID:26745530
Quality assessment and optimization of purified protein samples: why and how? PMID:25547134
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
Small molecule annotation for the Protein Data Bank. PMID:25425036
Computational methods for analysis and inference of kinase/inhibitor relationships. PMID:25071826
The future of crystallography in drug discovery. PMID:24372145
PDBe: Protein Data Bank in Europe. PMID:24288376 -
Safeguarding the integrity of protein archive
PubMed citations: 5.
5 articles citing: Safeguarding the integrity of protein archive
The data universe of structural biology. PMID:32695409
The Protein Data Bank archive as an open data resource. PMID:25062767
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
PDBe: Protein Data Bank in Europe. PMID:21045060 - http://dx.doi.org/10.1038/nsb1203-980
- http://dx.doi.org/10.1038%2Fnbt0807-845
- http://doi.org/10.1007/s12033-008-9127-7
- http://dx.doi.org/10.1038%2F543179a
- http://dx.doi.org/10.1101%2F110825
- http://dx.doi.org/10.1007%2F978-1-4939-7000-1
- http://dx.doi.org/10.1107%2F97809553602060000896
- http://dx.doi.org/10.1093/nar/28.1.235
Tags:
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
biology
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
proteomics
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
x-ray structures
metasource: re3data.org
version: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
structural biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
electron microscopy
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
nmr
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:22.453921
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: wwPDB; Worldwide Protein Data Bank; DOI: https://doi.org/10.25504/FAIRsharing.mckkb4; Last edited: April 26, 2021, 4:04 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
biology
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
proteomics
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
x-ray structures
metasource: re3data.orgversion: re3data.org: Worldwide Protein Data Bank; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3462V last accessed: 2022-11-04
structural biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
electron microscopy
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
nmr
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
protein structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:22.453921
dna protein protein structure rna molecular biology proteins proteomics x-ray structures structural biology electron microscopy nmr protein structure analysis
Need help integrating and/or managing biomedical data?