Protein Data Bank in Europe - Knowledge Base
Names
More detailed information about this field from each metasource.
Protein Data Bank in Europe - Knowledge Base
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
pdbe-kb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
Names
More detailed information about this field from each metasource.
Protein Data Bank in Europe - Knowledge Base
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
pdbe-kb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
Names
More detailed information about this field from each metasource.
Protein Data Bank in Europe - Knowledge Base
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
pdbe-kb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and a diverse group of bioinformatics resources and research teams. The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research.
Description
More detailed information about this field from each metasource.
PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and a diverse group of bioinformatics resources and research teams. The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research.
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Protein Data Bank in Europe - Knowledge Base
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
Webpage:
http://pdbe-kb.orgWebpage
More detailed information about this field from each metasource.
http://pdbe-kb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
https://pdbe-kb.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
Licence:
Name: EMBL-EBI Terms of UseLicence name
More detailed information about this field from each metasource.
EMBL-EBI Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Licence URL
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/about/terms-of-use
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
PMID: 30445541
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB: a community-driven resource for structural and functional annotations
PMID: 31584092
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB: collaboratively defining the biological context of structural data
PMID: 34755867
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
Publications
More detailed information about this field from each metasource.
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
PMID: 30445541
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB: a community-driven resource for structural and functional annotations
PMID: 31584092
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PDBe-KB: collaboratively defining the biological context of structural data
PMID: 34755867
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
-
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
PubMed citations: 55.
55 articles citing: SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
OBI: A computational tool for the analysis and systematization of the positive selection in proteins. PMID:35910305
Global Analysis of Deep Learning Prediction Using Large-Scale In-House Kinome-Wide Profiling Data. PMID:35694454
The 3D mutational constraint on amino acid sites in the human proteome. PMID:35672414
PepNN: a deep attention model for the identification of peptide binding sites. PMID:35618814
Developing Community Resources for Nucleic Acid Structures. PMID:35455031
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. PMID:35240125
An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. PMID:35210353
Localpdb- a Python package to manage protein structures and their annotations. PMID:35199148
Secondary Structures of Proteins Follow Menzerath-Altmann Law. PMID:35163493
Harnessing protein folding neural networks for peptide-protein docking. PMID:35013344
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
Slowest-first protein translation scheme: Structural asymmetry and co-translational folding. PMID:34813729
DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence. PMID:34765094
PDBe-KB: collaboratively defining the biological context of structural data. PMID:34755867
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data. PMID:34664328
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. PMID:34606614
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences. PMID:34228733
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
Completeness and Consistency in Structural Domain Classifications. PMID:34179613
Uncovering of cytochrome P450 anatomy by SecStrAnnotator. PMID:34117311
PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data. PMID:34081107
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
ModFlex: Towards Function Focused Protein Modeling. PMID:33972023
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
The Protein Data Bank Archive. PMID:33950382
From chemoproteomic-detected amino acids to genomic coordinates: insights into precise multi-omic data integration. PMID:33599394
Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants. PMID:33502607
In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. PMID:33491328
RCSB Protein Data Bank 1D Tools and Services. PMID:33313665
Data sets on human histone interaction networks. PMID:33299912
Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins. PMID:33291838
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PMID:33253214
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. PMID:33237313
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. PMID:33196841
Human Histone Interaction Networks: An Old Concept, New Trends. PMID:33098859
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. PMID:32997198
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. PMID:32776019
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. PMID:32297936
Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases. PMID:32133993
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals. PMID:32123117
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. PMID:31724711
Ensembl 2020. PMID:31691826
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. PMID:31581775
PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants. PMID:31075275
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
Finding enzyme cofactors in Protein Data Bank. PMID:30759194
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657 -
PDBe-KB: a community-driven resource for structural and functional annotations
PubMed citations: 42.
42 articles citing: PDBe-KB: a community-driven resource for structural and functional annotations
Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory. PMID:35869530
Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. PMID:35802469
Adamant: a JSON schema-based metadata editor for research data management workflows. PMID:35707001
canSAR chemistry registration and standardization pipeline. PMID:35643512
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. PMID:35641150
3DLigandSite: structure-based prediction of protein-ligand binding sites. PMID:35412635
Search and sequence analysis tools services from EMBL-EBI in 2022. PMID:35412617
Localpdb- a Python package to manage protein structures and their annotations. PMID:35199148
Databases for intrinsically disordered proteins. PMID:35102880
Iron dysregulation in COVID-19 and reciprocal evolution of SARS-CoV-2: Natura nihil frustra facit. PMID:34997606
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. PMID:34850135
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
Ensembl 2022. PMID:34791404
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. PMID:34791371
PDBe-KB: collaboratively defining the biological context of structural data. PMID:34755867
Priority index: database of genetic targets in immune-mediated disease. PMID:34751399
NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors. PMID:34549102
Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma. PMID:34465776
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. PMID:34301175
2DProts: Database of Family-Wide Protein Secondary Structure Diagrams. PMID:34244700
Understanding the structural details of APOBEC3-DNA interactions using graph-based representations. PMID:34235473
An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor. PMID:34174194
PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data. PMID:34081107
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. PMID:33956157
Online biophysical predictions for SARS-CoV-2 proteins. PMID:33892639
Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays. PMID:33453392
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
High-performance macromolecular data delivery and visualization for the web. PMID:33263322
Diamond Light Source: contributions to SARS-CoV-2 biology and therapeutics. PMID:33248689
From examining the relationship between (corona)viral adhesins and galectins to glyco-perspectives. PMID:33248129
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:33219674
Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. PMID:32404905
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. PMID:32297936
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
The Dundee Resource for Sequence Analysis and Structure Prediction. PMID:31710725
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
ELM-the eukaryotic linear motif resource in 2020. PMID:31680160 -
PDBe-KB: collaboratively defining the biological context of structural data
PubMed citations: 3.
3 articles citing: PDBe-KB: collaboratively defining the biological context of structural data
Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies. PMID:35480897
Role of genomics in combating COVID-19 pandemic. PMID:35248659
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
Tags:
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein folding
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
biophysics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
genetic variation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
protein structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
molecular biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:41.124743
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein folding
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PDBe-KB; Protein Data Bank in Europe - Knowledge Base; DOI: https://doi.org/10.25504/FAIRsharing.sFzdV7; Last edited: April 24, 2020, 3:45 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
biophysics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
genetic variation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
protein structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
molecular biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:41.124743
protein protein folding protein structure structure biophysics genetic variation protein structure analysis small molecule molecular biology
Need help integrating and/or managing biomedical data?