FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

PDBsum overview of macromolecular structures
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.885885

pdbsum
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.885885

Other names: PDBsum, PDBsum overview of macromolecular structures, pdbsum

PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

Webpage:

http://www.ebi.ac.uk/pdbsum

Licence:

Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
URL: http://opendatacommons.org/licenses/pddl/1.0/

Publications:

Publications
More detailed information about this field from each metasource.

PDBsum: Structural summaries of PDB entries
PMID: 28875543
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

PDBsum new things
PMID: 18996896
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

PDBsum additions
PMID: 24153109
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.885885

http://dx.doi.org/10.1093/nar/gkt940
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

PDBsum: Structural summaries of PDB entries PubMed citations: 265.

265 articles citing: PDBsum: Structural summaries of PDB entries

In silico design of a multi-epitope vaccine against HPV16/18. PMID:35918631
Augmenting apoptosis-mediated anticancer activity of lactoperoxidase and lactoferrin by nanocombination with copper and iron hybrid nanometals. PMID:35915221
Purification and Characterization of a Novel Extracellular Haloprotease Vpr from Bacillus licheniformis Strain KB111. PMID:35910276
Urtica dioica Agglutinin: A plant protein candidate for inhibition of SARS-COV-2 receptor-binding domain for control of Covid19 Infection. PMID:35901082
Immunoinformatic Approach to Contrive a Next Generation Multi-Epitope Vaccine Against Achromobacter xylosoxidans Infections. PMID:35899213
Genome-Wide Identification, Characterization, and Expression Analysis Related to Low-Temperature Stress of the CmGLP Gene Family in Cucumis melo L. PMID:35897766
Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease. PMID:35891436
The β2-Subunit (AMOG) of Human Na+, K+-ATPase Is a Homophilic Adhesion Molecule. PMID:35887102
Conformational changes in the catalytic region are responsible for heat-induced activation of hyperthermophilic homoserine dehydrogenase. PMID:35835834
Computer-Aided Multi-Epitope Vaccine Design against Enterobacter xiangfangensis. PMID:35805383
Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction. PMID:35779308
Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. PMID:35745579
Deep Ensemble Learning with Atrous Spatial Pyramid Networks for Protein Secondary Structure Prediction. PMID:35740899
Improvement of Fusel Alcohol Production by Engineering of the Yeast Branched-Chain Amino Acid Aminotransaminase. PMID:35699439
High-affinity anti-Arc nanobodies provide tools for structural and functional studies. PMID:35671319
GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro. PMID:35667152
Reversible modification of mitochondrial ADP/ATP translocases by paired Legionella effector proteins. PMID:35653564
Substantiation of propitious "Enzybiotic" from two novel bacteriophages isolated from a wastewater treatment plant in Qatar. PMID:35641576
Design of a Multi-Epitope Vaccine against Tropheryma whipplei Using Immunoinformatics and Molecular Dynamics Simulation Techniques. PMID:35632446
Consensus Enolase of Trypanosoma Cruzi: Evaluation of Their Immunogenic Properties Using a Bioinformatics Approach. PMID:35629412
An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2. PMID:35625526
Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. PMID:35558562
Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach. PMID:35545650
Development of multivalent vaccine targeting M segment of Crimean Congo Hemorrhagic Fever Virus (CCHFV) using immunoinformatic approaches. PMID:35531180
Protein interactions with metallothionein-3 promote vectorial active transport in human proximal tubular cells. PMID:35503771
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
In silico Docking Analysis for Blocking JUNO-IZUMO1 Interaction Identifies Two Small Molecules that Block in vitro Fertilization. PMID:35478965
Identification of Zinc-Binding Inhibitors of Matrix Metalloproteinase-9 to Prevent Cancer Through Deep Learning and Molecular Dynamics Simulation Approach. PMID:35463960
The Molecular Basis of the Effect of Temperature on the Structure and Function of SARS-CoV-2 Spike Protein. PMID:35463957
Identification of Putative Elicitors From Plant Root Exudates Responsible for PsoR Activation in Plant-Beneficial Pseudomonas spp. by Docking and Molecular Dynamics Simulation Approaches to Decipher Plant-Microbe Interaction. PMID:35463415
In Silico Analysis of the Antagonist Effect of Enoxaparin on the ApoE4-Amyloid-Beta (Aβ) Complex at Different pH Conditions. PMID:35454088
High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1. PMID:35435730
In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. PMID:35423962
Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. PMID:35414157
Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase. PMID:35410329
Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease. PMID:35408866
Inhibition of Filamentous Thermosensitive Mutant-Z Protein in Bacillus subtilis by Cyanobacterial Bioactive Compounds. PMID:35335270
SARS-CoV-2 Proteins Interact with Alpha Synuclein and Induce Lewy Body-like Pathology In Vitro. PMID:35328814
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. PMID:35317722
Novel In Silico mRNA vaccine design exploiting proteins of M. tuberculosis that modulates host immune responses by inducing epigenetic modifications. PMID:35301360
The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane. PMID:35300425
Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis. PMID:35290794
Inhibitory Effects of Bacterial Silk-like Biopolymer on Herpes Simplex Virus Type 1, Adenovirus Type 7 and Hepatitis C Virus Infection. PMID:35225980
Structure and assembly of the S-layer in C. difficile. PMID:35217634
Improved SARS-CoV-2 main protease high-throughput screening assay using a 5-carboxyfluorescein substrate. PMID:35182525
Peptide-Based Vaccines for Tuberculosis. PMID:35173740
Structural and functional insights into the inhibition of human voltage-gated sodium channels by μ-conotoxin KIIIA disulfide isomers. PMID:35167877
Autoxidation Products of the Methanolic Extract of the Leaves of Combretum micranthum Exert Antiviral Activity against Tomato Brown Rugose Fruit Virus (ToBRFV). PMID:35164024
X-ray Crystal Structure Analysis of VHH-Protein Antigen Complexes. PMID:35157291
Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2. PMID:35138508
Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. PMID:35137487
Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. PMID:35110564
A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation. PMID:35062878
Analysis of 272 Genetic Variants in the Upgraded Interactive FXI Web Database Reveals New Insights into FXI Deficiency. PMID:35059554
Characterization of Cyclophilin from Thaumarchaeota Nitrosopumilus maritimus: Implications on the Diversity of Chaperone-like Activity in the Archaeal Domain. PMID:35036680
Structural characterization of human importin alpha 7 in its cargo-free form at 2.5 Å resolution. PMID:35013395
Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach. PMID:35011492
Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis. PMID:35011319
Group depositions to the Protein Data Bank need adequate presentation and different archiving protocol. PMID:35000237
In vitro characterization of a small molecule PD-1 inhibitor that targets the PD-l/PD-L1 interaction. PMID:34996924
Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex. PMID:34959589
Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. PMID:34948055
AlphaFold-Predicted Structures of KCTD Proteins Unravel Previously Undetected Relationships among the Members of the Family. PMID:34944504
Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. PMID:34943225
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. PMID:34929376
Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. PMID:34914928
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
In Silico Analysis of Inhibiting Papain-like Protease from SARS-CoV-2 by Using Plant-Derived Peptides. PMID:34903959
Structure, mechanism, and inhibition of Hedgehog acyltransferase. PMID:34890564
Structural Modelling of KCNQ1 and KCNH2 Double Mutant Proteins, Identified in Two Severe Long QT Syndrome Cases, Reveals New Insights into Cardiac Channelopathies. PMID:34884666
Pan-Genome Reverse Vaccinology Approach for the Design of Multi-Epitope Vaccine Construct against Escherichia albertii. PMID:34884620
Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1. PMID:34870595
Structure and Mutations of SARS-CoV-2 Spike Protein: A Focused Overview. PMID:34856799
A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. PMID:34853389
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PMID:34843456
Whole Exome Sequencing Study in a Family with Type 2 Diabetes Mellitus. PMID:34815695
High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. PMID:34812732
Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens. PMID:34785651
PDBsum extras: SARS-CoV-2 and AlphaFold models. PMID:34779073
A Computational Reverse Vaccinology Approach for the Design and Development of Multi-Epitopic Vaccine Against Avian Pathogen Mycoplasma gallisepticum. PMID:34765664
APPRIS: selecting functionally important isoforms. PMID:34755885
Development of an in silico multi-epitope vaccine against SARS-COV-2 by précised immune-informatics approaches. PMID:34746365
A Novel Homozygous Missense Mutation in the Zinc Finger DNA Binding Domain of GLI1 Causes Recessive Post-Axial Polydactyly. PMID:34721536
Functional Annotation from Structural Homology. PMID:34718998
Structural and Evolutionary Insights Into the Binding of Host Receptors by the Rabies Virus Glycoprotein. PMID:34708003
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
Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. PMID:34681096
Potential efficacy of existing drug molecules against severe fever with thrombocytopenia syndrome virus: an in silico study. PMID:34675254
Implications of divergence of methionine adenosyltransferase in archaea. PMID:34655277
Epitope-specific anti-PrP antibody toxicity: a comparative in-silico study of human and mouse prion proteins. PMID:34632945
Bacteriophage Twort protein Gp168 is a β-clamp inhibitor by occupying the DNA sliding channel. PMID:34614154
Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. PMID:34605434
Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation. PMID:34571756
Molecular basis for ATPase-powered substrate translocation by the Lon AAA+ protease. PMID:34563541
Capsid Structure of Anabaena Cyanophage A-1(L). PMID:34549983
Analysing the impact of the two most common SARS-CoV-2 nucleocapsid protein variants on interactions with membrane protein in silico. PMID:34542740
RetS inhibits Pseudomonas aeruginosa biofilm formation by disrupting the canonical histidine kinase dimerization interface of GacS. PMID:34529974
Encephalopathy-causing mutations in Gβ1 (GNB1) alter regulation of neuronal GIRK channels. PMID:34522861
Computational Design of a Multi-epitope Vaccine Against Clostridium chauvoei: An Immunoinformatics Approach. PMID:34493934
Identification and In Silico Characterization of Novel Helicobacter pylori Glucose-6-Phosphate Dehydrogenase Inhibitors. PMID:34443540
DNA interference states of the hypercompact CRISPR-CasΦ effector. PMID:34381246
Finding inhibitors for PCSK9 using computational methods. PMID:34351937
Characterization of a Stable Form of Carboxypeptidase G2 (Glucarpidase), a Potential Biobetter Variant, From Acinetobacter sp. 263903-1. PMID:34268672
In silico designing of vaccine candidate against Clostridium difficile. PMID:34244557
Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase. PMID:34235541
Computational identification and characterization of antigenic properties of Rv3899c of Mycobacterium tuberculosis and its interaction with human leukocyte antigen (HLA). PMID:34228167
Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis. PMID:34208663
An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population. PMID:34205992
A 3.4-Å cryo-electron microscopy structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles. PMID:34192263
Structure of the Arabidopsis thaliana glutamate receptor-like channel GLR3.4. PMID:34161757
Computational study to discover potent phytochemical inhibitors against drug target, squalene synthase from Leishmania donovani. PMID:34141935
Crystal structure of the anti-CRISPR repressor Aca2. PMID:34116143
Crystal Structure of the [4Fe-4S] Cluster-Containing Adenosine-5'-phosphosulfate Reductase from Mycobacterium tuberculosis. PMID:34095667
Multi-epitope-Based Vaccine Designed by Targeting Cytoadherence Proteins of Mycoplasma gallisepticum. PMID:34095666
Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: A molecular modeling approach. PMID:34075338
PilB from Streptococcus sanguinis is a bimodular type IV pilin with a direct role in adhesion. PMID:34031252
ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer. PMID:34012037
ProteoVision: web server for advanced visualization of ribosomal proteins. PMID:33999189
Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc. PMID:33989344
Identification of benzamide inhibitors of histone deacetylase 1 from Babesia and Theileria species via high-throughput virtual screening and molecular dynamics simulations. PMID:33987736
Quantum biochemistry, molecular docking, and dynamics simulation revealed synthetic peptides induced conformational changes affecting the topology of the catalytic site of SARS-CoV-2 main protease. PMID:33949286
Buried Kex2 Sites in Glargine Precursor Aggregates Prevent Its Intracellular Processing in Pichia pastoris Muts Strains and the Effect of Methanol-Feeding Strategy and Induction Temperature on Glargine Precursor Production Parameters. PMID:33931817
A highly conserved 310 helix within the kinesin motor domain is critical for kinesin function and human health. PMID:33931448
Molecular Simulation-Based Investigation of Highly Potent Natural Products to Abrogate Formation of the nsp10-nsp16 Complex of SARS-CoV-2. PMID:33919870
Structure and Dynamics of an Archeal Monoglyceride Lipase from Palaeococcus ferrophilus as Revealed by Crystallography and In Silico Analysis. PMID:33916727
Inhibition of SARS-CoV-2 3CL Mpro by Natural and Synthetic Inhibitors: Potential Implication for Vaccine Production Against COVID-19. PMID:33912587
A unique view of SARS-CoV-2 through the lens of ORF8 protein. PMID:33872970
The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms. PMID:33815739
Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase. PMID:33815691
Structure and Location of Protein Sites Binding Self-Associated Congo Red Molecules with Intercalated Drugs as Compact Ligands-Theoretical Studies. PMID:33810400
Overexpression of an Agave Phosphoenolpyruvate Carboxylase Improves Plant Growth and Stress Tolerance. PMID:33800849
Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. PMID:33795718
Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases. PMID:33782435
In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function. PMID:33730245
SARM1 is a metabolic sensor activated by an increased NMN/NAD+ ratio to trigger axon degeneration. PMID:33657413
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. PMID:33633170
Structural insights into the intermolecular interaction of the adhesin SdrC in the pathogenicity of Staphylococcus aureus. PMID:33620037
De novo design of transmembrane β barrels. PMID:33602829
Rational design of multi epitope-based subunit vaccine by exploring MERS-COV proteome: Reverse vaccinology and molecular docking approach. PMID:33534822
In silico characterization and structural modeling of bacterial metalloprotease of family M4. PMID:33528696
Identification of potential SARS-CoV-2 entry inhibitors by targeting the interface region between the spike RBD and human ACE2. PMID:33493919
Biochemical Characterization and Functional Analysis of Heat Stable High Potential Protease of Bacillus amyloliquefaciens Strain HM48 from Soils of Dachigam National Park in Kashmir Himalaya. PMID:33477596
Designing a next generation multi-epitope based peptide vaccine candidate against SARS-CoV-2 using computational approaches. PMID:33457172
In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach. PMID:33454889
Biophysical characterization of the ETV6 PNT domain polymerization interfaces. PMID:33450226
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. PMID:33450012
Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. PMID:33430354
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts. PMID:33357443
Structure and dynamics of membrane protein in SARS-CoV-2. PMID:33353499
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. PMID:33347301
S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. PMID:33339190
Distinct GluN1 and GluN2 Structural Determinants for Subunit-Selective Positive Allosteric Modulation of N-Methyl-d-aspartate Receptors. PMID:33326224
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. PMID:33318575
The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein. PMID:33263569
Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues. PMID:33203760
The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking. PMID:33199981
Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases. PMID:33187094
Multitask ATPases (NBDs) of bacterial ABC importers type I and their interspecies exchangeability. PMID:33177617
Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain-human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2. PMID:33146070
Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics on Legionella phagosomes. PMID:33136002
Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis. PMID:33135671
Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 Mpro, using molecular docking and dynamics simulation studies. PMID:33131721
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. PMID:33106425
Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAA Receptor by Molecular Modeling. PMID:33041802
Structure of the Arabidopsis Glutamate Receptor-like Channel GLR3.2 Ligand-Binding Domain. PMID:33027636
Full-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer. PMID:32997652
Global distribution of single amino acid polymorphisms in Plasmodium vivax Duffy-binding-like domain and implications for vaccine development efforts. PMID:32993415
Predicting binding sites from unbound versus bound protein structures. PMID:32985584
Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2. PMID:32938504
Evidence that immunization with TP0751, a bipartite Treponema pallidum lipoprotein with an intrinsically disordered region and lipocalin fold, fails to protect in the rabbit model of experimental syphilis. PMID:32936831
The Structure of the Cysteine-Rich Domain of Plasmodium falciparum P113 Identifies the Location of the RH5 Binding Site. PMID:32900802
Enhanced Antigiardial Effect of Omeprazole Analog Benzimidazole Compounds. PMID:32882836
Crystal structures of native cytochrome c6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization. PMID:32880593
An epoxide hydrolase from endophytic Streptomyces shows unique structural features and wide biocatalytic activity. PMID:32876062
Influence of Catecholamines (Epinephrine/Norepinephrine) on Biofilm Formation and Adhesion in Pathogenic and Probiotic Strains of Enterococcus faecalis. PMID:32849320
Viroinformatics approach to explore the inhibitory mechanism of existing drugs repurposed to fight against COVID-19. PMID:32841640
Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences. PMID:32832263
Homology Modeling and Probable Active Site Cavity Prediction of Uncharacterized Arsenate Reductase in Bacterial spp. PMID:32809107
Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages. PMID:32730844
A convenient protein library for spectroscopic calibrations. PMID:32728409
Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. PMID:32723797
Plant Defensins from a Structural Perspective. PMID:32722628
Synthetic Peptides as a Promising Alternative to Control Viral Infections in Atlantic Salmon. PMID:32717804
A molecular docking study revealed that synthetic peptides induced conformational changes in the structure of SARS-CoV-2 spike glycoprotein, disrupting the interaction with human ACE2 receptor. PMID:32693122
Deamidated Human Triosephosphate Isomerase is a Promising Druggable Target. PMID:32679775
Structure of the Regulatory Cytosolic Domain of a Eukaryotic Potassium-Chloride Cotransporter. PMID:32679039
A candidate multi-epitope vaccine against SARS-CoV-2. PMID:32616763
Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine. PMID:32583729
Constitutive expression of Asparaginase in Gossypium hirsutum triggers insecticidal activity against Bemisia tabaci. PMID:32488033
Legionella effector AnkX displaces the switch II region for Rab1b phosphocholination. PMID:32440549
Structural basis for membrane insertion by the human ER membrane protein complex. PMID:32439656
A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM. PMID:32424347
Molecular Modelling and Insilico Engineering of PapMV-CP Towards Display and Development of Capripox Viral Like Particles Based on Immunogenic P32 Envelop Protein is the Homologous of the Vaccinia-Viral H3L Gene: An Insilico Approach. PMID:32421016
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. PMID:32402084
State-of-the-art tools unveil potent drug targets amongst clinically approved drugs to inhibit helicase in SARS-CoV-2. PMID:32399096
PDZ Domains as Drug Targets. PMID:32313833
Protein-protein interaction of Rv0148 with Htdy and its predicted role towards drug resistance in Mycobacterium tuberculosis. PMID:32295519
Minimally altering a critical kinase for low-phytate maize. PMID:32286385
Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase. PMID:32266873
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. PMID:32243832
NMDA receptor channel gating control by the pre-M1 helix. PMID:32221541
Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM. PMID:32170016
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. PMID:32164553
Structure-Function Studies and Mechanism of Action of Snake Venom L-Amino Acid Oxidases. PMID:32158389
Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-β-1,4-mannanase. PMID:32139511
An insight into structural plasticity and conformational transitions of transcriptional co-activator Sus1. PMID:32134955
Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. PMID:32079722
Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases. PMID:32079302
Conformational flexibility within the small domain of human serine racemase. PMID:32039887
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
Identification of tunnels as in potato hydrolases. PMID:32025157
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Computational prediction of active sites and ligands in different AHL quorum quenching lactonases and acylases. PMID:32020908
Alternative Structures of α-Synuclein. PMID:32019169
Affinity-matured variants derived from nimotuzumab keep the original fine specificity and exhibit superior biological activity. PMID:31988343
Dynamic properties of oligomers that characterize low-frequency normal modes. PMID:31984175
Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis. PMID:31886928
Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex. PMID:31819272
Considerations on the Rational Design of Covalently Conjugated Cell-Penetrating Peptides (CPPs) for Intracellular Delivery of Proteins: A Guide to CPP Selection Using Glucarpidase as the Model Cargo Molecule. PMID:31779220
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana. PMID:31681359
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. PMID:31645552
Insights revealed by the co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer protein Ypd1 and the receiver domain of its downstream response regulator Ssk1. PMID:31642125
Rigorous sampling of docking poses unveils binding hypothesis for the halogenated ligands of L-type Amino acid Transporter 1 (LAT1). PMID:31636293
Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins. PMID:31626803
Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein. PMID:31615004
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
VarSite: Disease variants and protein structure. PMID:31606900
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
Vigilin protein Vgl1 is required for heterochromatin-mediated gene silencing in Schizosaccharomyces pombe. PMID:31554660
Different Synergy in Amyloids and Biologically Active Forms of Proteins. PMID:31505841
The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature. PMID:31417084
Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. PMID:31410573
Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea (Cajanus Cajan L.). PMID:31295921
3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns. PMID:31261733
Enzyme activity and structural features of three single-domain phloem cyclophilins from Brassica napus. PMID:31249367
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Structure of a functional cap-binding domain in Rift Valley fever virus L protein. PMID:31136637
Modeling of Protein⁻Protein Interactions in Cytokinin Signal Transduction. PMID:31035389
Periplasmic Nanobody-APEX2 Fusions Enable Facile Visualization of Ebola, Marburg, and Mĕnglà virus Nucleoproteins, Alluding to Similar Antigenic Landscapes among Marburgvirus and Dianlovirus. PMID:31010013
A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius. PMID:30948713
Chain-Branched Polyhydroxylated Octahydro-1H-Indoles as Potential Leads against Lysosomal Storage Diseases. PMID:30934879
Tethering soluble meprin α in an enzyme complex to the cell surface affects IBD-associated genes. PMID:30916990
Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution. PMID:30894496
Cross-Species Analysis of Glycosaminoglycan Binding Proteins Reveals Some Animal Models Are "More Equal" than Others. PMID:30845788
Identification of the laccase-like multicopper oxidase gene family of sweet cherry (Prunus avium L.) and expression analysis in six ancient Tuscan varieties. PMID:30837484
Structural introspection of a putative fluoride transporter in plants. PMID:30800614
Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon. PMID:30789963
Structure-Based Engineering of Amidase from Pantoea sp. for Efficient 2-Chloronicotinic Acid Biosynthesis. PMID:30578259
Search of Allosteric Inhibitors and Associated Proteins of an AKT-like Kinase from Trypanosoma cruzi. PMID:30544836
A comprehensive in silico characterization of bacterial signal peptides for the excretory production of Anabaena variabilis phenylalanine ammonia lyase in Escherichia coli. PMID:30498661
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Strategic single point mutation yields a solvent- and salt-stable transaminase from Virgibacillus sp. in soluble form. PMID:30401905
SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. PMID:30087931
Structural and functional analysis of cystatin E reveals enzymologically relevant dimer and amyloid fibril states. PMID:29967063
Novel Insights from Comparative In Silico Analysis of Green Microalgal Cellulases. PMID:29914107
Bioinformatics analysis of CYP1B1 mutation hotspots in Chinese primary congenital glaucoma patients. PMID:29903728
Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65. PMID:29659842
Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance. PMID:29587635
Crystal structure of Brugia malayi venom allergen-like protein-1 (BmVAL-1), a vaccine candidate for lymphatic filariasis. PMID:29501266
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. PMID:29145643
Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. PMID:29119630
PDBsum new things PubMed citations: 239.

239 articles citing: PDBsum new things

In silico design of a multi-epitope vaccine against HPV16/18. PMID:35918631
A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity. PMID:35902770
Recognition of the TDP-43 nuclear localization signal by importin α1/β. PMID:35767952
S-Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis. PMID:35749503
Novel Dihydropyrimidinone Derivatives as Potential P-Glycoprotein Modulators. PMID:35601326
Purification, characterization and functional site prediction of the vaccinia-related kinase 2A small transmembrane domain. PMID:35518920
An in silico approach unveils the potential of antiviral compounds in preclinical and clinical trials as SARS-CoV-2 omicron inhibitors. PMID:35475118
First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. PMID:35368742
Investigation of Plant Antimicrobial Peptides against Selected Pathogenic Bacterial Species Using a Peptide-Protein Docking Approach. PMID:35355819
Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PMID:35341049
Candidate Therapeutics by Screening for Multitargeting Ligands: Combining the CB2 Receptor With CB1, PPARγ and 5-HT4 Receptors. PMID:35295337
Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3. PMID:35278476
Differential recognition of canonical NF-κB dimers by Importin α3. PMID:35260573
Human IL-2Rɑ subunit binding modulation of IL-2 through a decline in electrostatic interactions: A computational and experimental approach. PMID:35213635
Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV. PMID:35153334
Tracking the circulating SARS-CoV-2 variant of concern in South Africa using wastewater-based epidemiology. PMID:35064174
Preparation, urease inhibition mechanisms, and anti-Helicobacter pylori activities of hesperetin-7-rhamnoglucoside. PMID:35024644
Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population. PMID:34960205
Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. PMID:34955621
Development of a Candidate Multi-Epitope Subunit Vaccine against Klebsiella aerogenes: Subtractive Proteomics and Immuno-Informatics Approach. PMID:34835304
High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. PMID:34812732
PDBsum extras: SARS-CoV-2 and AlphaFold models. PMID:34779073
Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells. PMID:34696326
Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens. PMID:34696187
An in-depth in silico and immunoinformatics approach for designing a potential multi-epitope construct for the effective development of vaccine to combat against SARS-CoV-2 encompassing variants of concern and interest. PMID:34352457
Novel heterocyclic 1,3,4-oxadiazole derivatives of fluoroquinolones as a potent antibacterial agent: Synthesis and computational molecular modeling. PMID:34341943
Cryo-EM structure of the periplasmic tunnel of T7 DNA-ejectosome at 2.7 Å resolution. PMID:34214465
Interaction of Temporin-L Analogues with the E. coli FtsZ Protein. PMID:34208230
ProteoVision: web server for advanced visualization of ribosomal proteins. PMID:33999189
CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. PMID:33949948
Molecular Simulation-Based Investigation of Highly Potent Natural Products to Abrogate Formation of the nsp10-nsp16 Complex of SARS-CoV-2. PMID:33919870
In Silico Characterization of Growth Differentiation Factors as Inhibitors of TNF-Alpha and IL-6 in Immune-Mediated Inflammatory Disease Rheumatoid Arthritis. PMID:33855071
Hesperidin Targets Leishmania donovani Sterol C-24 Reductase to Fight against Leishmaniasis. PMID:33817470
Assessment of the Antileishmanial Potential of Cassia fistula Leaf Extract. PMID:33521470
Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide. PMID:33495563
In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach. PMID:33454889
Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. PMID:33351863
Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. PMID:33077836
Repurposing of the approved small molecule drugs in order to inhibit SARS-CoV-2 S protein and human ACE2 interaction through virtual screening approaches. PMID:32969333
Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects. PMID:32820052
Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatis. PMID:32751237
Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach. PMID:32521680
Spectroscopic and Molecular Modeling Investigation on the Interaction between Folic Acid and Bovine Lactoferrin from Encapsulation Perspectives. PMID:32512783
Negative allosteric modulation of GluN1/GluN3 NMDA receptors. PMID:32389749
Leishmanicidal Activity of an In Silico-Screened Novel Inhibitor against Ascorbate Peroxidase of Leishmania donovani. PMID:32366716
Comparative modeling and mutual docking of structurally uncharacterized heat shock protein 70 and heat shock factor-1 proteins in water buffalo. PMID:32095057
Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B. PMID:31893251
Evaluation of Anti-inflammatory and Regenerative Efficiency of Naringin and Naringenin in Degenerated Human Nucleus Pulposus Cells: Biological and Molecular Modeling Studies. PMID:31575107
Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor. PMID:31391779
Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA. PMID:31227715
Molecular Architecture of the Inositol Phosphatase Siw14. PMID:30548067
The Structure of the Bifunctional Everninomicin Biosynthetic Enzyme EvdMO1 Suggests Independent Activity of the Fused Methyltransferase-Oxidase Domains. PMID:30525509
Resistance determination of the ACCase-inhibiting herbicide of clodinafop propargyl in Avena ludoviciana (Durieu), and study of their interaction using molecular docking and simulation. PMID:30448893
Novel regulatory mechanism of establishment genes of conjugative plasmids. PMID:30380104
Bonsai Gelsolin Survives Heat Induced Denaturation by Forming β-Amyloids which Leach Out Functional Monomer. PMID:30135452
Differential Conformational Dynamics Encoded by the Linker between Quasi RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein H. PMID:30122033
Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. PMID:30082873
A structurally derived model of subunit-dependent NMDA receptor function. PMID:29917241
Genetic characterization of Chikungunya virus 2009 isolates from South India. PMID:29785069
Disruption of the open conductance in the β-tongue mutants of Cytolysin A. PMID:29491391
The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor. PMID:29242355
The crystal structure of pseudokinase PEAK1 (Sugen kinase 269) reveals an unusual catalytic cleft and a novel mode of kinase fold dimerization. PMID:29212708
Zona pellucida-binding protein 2 (ZPBP2) and several proteins containing BX7B motifs in human sperm may have hyaluronic acid binding or recognition properties. PMID:29126140
Mix-and-diffuse serial synchrotron crystallography. PMID:29123679
PDBsum: Structural summaries of PDB entries. PMID:28875543
X-ray crystallographic structure of a bacterial polysialyltransferase provides insight into the biosynthesis of capsular polysialic acid. PMID:28724897
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii. PMID:28512574
Structural Basis for Importin-α Binding of the Human Immunodeficiency Virus Tat. PMID:28490747
Structural and functional mapping of Rtg2p determinants involved in retrograde signaling and aging of Saccharomyces cerevisiae. PMID:28472157
Understanding human thiol dioxygenase enzymes: structure to function, and biology to pathology. PMID:28439920
Structural landscape of base pairs containing post-transcriptional modifications in RNA. PMID:28341704
Comparative visualization of protein secondary structures. PMID:28251875
Functional Evaluation of a De Novo GRIN2A Mutation Identified in a Patient with Profound Global Developmental Delay and Refractory Epilepsy. PMID:28126851
PICI: A web server with a multi-parametric algorithm for identifying interaction sites within protein complexes. PMID:28104965
The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans. PMID:27531750
Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication. PMID:27383630
Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway. PMID:27303801
Predicted 3D Model of the Rabies Virus Glycoprotein Trimer. PMID:27294109
Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. PMID:27153537
1.2 Å resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa. PMID:27139833
Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold. PMID:27090909
Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein. PMID:26980835
Atomic resolution probe for allostery in the regulatory thin filament. PMID:26957598
Characterization of heat induced spherulites of lysozyme reveals new insight on amyloid initiation. PMID:26926993
Characterization of DWARF14 Genes in Populus. PMID:26875827
Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. PMID:26787904
Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains. PMID:26735515
Discrete structural features among interface residue-level classes. PMID:26679043
Exploring the heat-induced structural changes of β-lactoglobulin -linoleic acid complex by fluorescence spectroscopy and molecular modeling techniques. PMID:26604382
Negative Feedbacks by Isoprenoids on a Mevalonate Kinase Expressed in the Corpora Allata of Mosquitoes. PMID:26566274
Monitoring the heat-induced structural changes of alkaline phosphatase by molecular modeling, fluorescence spectroscopy and inactivation kinetics investigations. PMID:26396374
The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD. PMID:26237511
Structure and vascular function of MEKK3-cerebral cavernous malformations 2 complex. PMID:26235885
Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. PMID:26192331
Structural analysis of ibuprofen binding to human adipocyte fatty-acid binding protein (FABP4). PMID:25664790
The strength and cooperativity of KIT ectodomain contacts determine normal ligand-dependent stimulation or oncogenic activation in cancer. PMID:25544564
Structural basis for the disruption of the cerebral cavernous malformations 2 (CCM2) interaction with Krev interaction trapped 1 (KRIT1) by disease-associated mutations. PMID:25525273
Intrinsic disorder drives N-terminal ubiquitination by Ube2w. PMID:25436519
A novel alkyl hydroperoxidase (AhpD) of Anabaena PCC7120 confers abiotic stress tolerance in Escherichia coli. PMID:25391500
Crystallographic study of the phosphoethanolamine transferase EptC required for polymyxin resistance and motility in Campylobacter jejuni. PMID:25286856
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. PMID:25185655
Isothiocyanate analogs targeting CD44 receptor as an effective strategy against colon cancer. PMID:25013352
Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions. PMID:25004977
Cloning, expression and characterization of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from Wolbachia endosymbiont of human lymphatic filarial parasite Brugia malayi. PMID:24941309
Structures and binding specificity of galactose- and mannose-binding lectins from champedak: differences from jackfruit lectins. PMID:24915077
Structural insights into the lipoprotein outer membrane regulator of penicillin-binding protein 1B. PMID:24808177
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. PMID:24646163
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Characterization of the proliferating cell nuclear antigen of Leishmania donovani clinical isolates and its association with antimony resistance. PMID:24614385
Genetically engineered synthetic miniaturized versions of Plasmodium falciparum UvrD helicase are catalytically active. PMID:24608129
The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding. PMID:24598754
Insights into the initiation of JC virus DNA replication derived from the crystal structure of the T-antigen origin binding domain. PMID:24586168
Structural and enzymatic characterization of a host-specificity determinant from Salmonella. PMID:24531472
C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability. PMID:24526385
Cardiac myosin binding protein-C: a structurally dynamic regulator of myocardial contractility. PMID:24469349
Structure of human PIR1, an atypical dual-specificity phosphatase. PMID:24447265
A tale of two drug targets: the evolutionary history of BACE1 and BACE2. PMID:24381583
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. PMID:24356774
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PMID:24348229
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. PMID:24319146
LigSearch: a knowledge-based web server to identify likely ligands for a protein target. PMID:24311580
The Structure-Function Linkage Database. PMID:24271399
Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I. PMID:24220130
Effect of intracellular loop 3 on intrinsic dynamics of human β2-adrenergic receptor. PMID:24206668
The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases. PMID:24206647
PDBsum additions. PMID:24153109
Poxviral protein A52 stimulates p38 mitogen-activated protein kinase (MAPK) activation by causing tumor necrosis factor receptor-associated factor 6 (TRAF6) self-association leading to transforming growth factor β-activated kinase 1 (TAK1) recruitment. PMID:24114841
Can inhibitor-resistant substitutions in the Mycobacterium tuberculosis β-Lactamase BlaC lead to clavulanate resistance?: a biochemical rationale for the use of β-lactam-β-lactamase inhibitor combinations. PMID:24060876
NMR structure and MD simulations of the AAA protease intermembrane space domain indicates peripheral membrane localization within the hexaoligomer. PMID:24055473
Structure of the Mtb CarD/RNAP β-lobes complex reveals the molecular basis of interaction and presents a distinct DNA-binding domain for Mtb CarD. PMID:24055315
Structure of the NheA component of the Nhe toxin from Bacillus cereus: implications for function. PMID:24040335
The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments. PMID:23957615
The structure of substrate-free 1,5-anhydro-D-fructose reductase from Sinorhizobium meliloti 1021 reveals an open enzyme conformation. PMID:23908025
β-Bulges: extensive structural analyses of β-sheets irregularities. PMID:23904395
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Analysis of dimerization of BTB-IVR domains of Keap1 and its interaction with Cul3, by molecular modeling. PMID:23847398
Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PMID:23785468
Scalable web services for the PSIPRED Protein Analysis Workbench. PMID:23748958
Structural dynamics flexibility informs function and evolution at a proteome scale. PMID:23745135
Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth. PMID:23715690
Gene identification and comparative molecular modeling of a Trypanosoma rangeli major surface protease. PMID:23584556
Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions. PMID:23555243
Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2. PMID:23527120
Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycH-YopH chaperone-effector complex. PMID:23519663
Novel dual cyclooxygenase and lipoxygenase inhibitors targeting hyaluronan-CD44v6 pathway and inducing cytotoxicity in colon cancer cells. PMID:23517721
Computational analysis of C-reactive protein for assessment of molecular dynamics and interaction properties. PMID:23494263
The insecticidal neurotoxin Aps III is an atypical knottin peptide that potently blocks insect voltage-gated sodium channels. PMID:23473802
In silico structural and functional characterization of the RSUME splice variants. PMID:23469069
Role of P-glycoprotein at the blood-testis barrier on adjudin distribution in the testis: a revisit of recent data. PMID:23397632
Atomic structure of dual-specificity phosphatase 26, a novel p53 phosphatase. PMID:23298255
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. PMID:23281852
Analysis of the costructure of the simian virus 40 T-antigen origin binding domain with site I reveals a correlation between GAGGC spacing and spiral assembly. PMID:23269808
Structural-functional studies of Burkholderia cenocepacia D-glycero-β-D-manno-heptose 7-phosphate kinase (HldA) and characterization of inhibitors with antibiotic adjuvant and antivirulence properties. PMID:23256532
Outer domain of HIV-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody VRC-PG04. PMID:23236069
Structure of aminodeoxychorismate synthase from Stenotrophomonas maltophilia. PMID:23230967
FMNL3 FH2-actin structure gives insight into formin-mediated actin nucleation and elongation. PMID:23222643
PDBTM: Protein Data Bank of transmembrane proteins after 8 years. PMID:23203988
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
Structure of the catalytic domain of the Salmonella virulence factor SseI. PMID:23151626
Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major. PMID:23151081
Influence of PAS domain flanking regions on oligomerisation and redox signalling by NifL. PMID:23056386
Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study. PMID:22970161
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. PMID:22948926
Structure of a tetrameric galectin from Cinachyrella sp. (ball sponge). PMID:22948917
Structure of a proteasome Pba1-Pba2 complex: implications for proteasome assembly, activation, and biological function. PMID:22930756
Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PMID:22761755
Leishmania donovani pteridine reductase 1: comparative protein modeling and protein-ligand interaction studies of the leishmanicidal constituents isolated from the fruits of Piper longum. PMID:22752544
Structure and activity of the only human RNase T2. PMID:22735700
Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant. PMID:22719917
Structure of p22 headful packaging nuclease. PMID:22715098
The human transporter associated with antigen processing: molecular models to describe peptide binding competent states. PMID:22700967
PBSword: a web server for searching similar protein-protein binding sites. PMID:22689645
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. PMID:22689386
Mapping the binding of GluN2B-selective N-methyl-D-aspartate receptor negative allosteric modulators. PMID:22596351
In silico assessment of potential druggable pockets on the surface of α1-antitrypsin conformers. PMID:22590577
The transcription factor AmrZ utilizes multiple DNA binding modes to recognize activator and repressor sequences of Pseudomonas aeruginosa virulence genes. PMID:22511872
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. PMID:22465017
Evidence of Fe3+ interaction with the plug domain of the outer membrane transferrin receptor protein of Neisseria gonorrhoeae: implications for Fe transport. PMID:22399131
Candida albicans possesses Sap7 as a pepstatin A-insensitive secreted aspartic protease. PMID:22384266
Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability. PMID:22374910
High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). PMID:22349223
Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system. PMID:22349221
Structure of the Yersinia pestis FabV enoyl-ACP reductase and its interaction with two 2-pyridone inhibitors. PMID:22244758
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. PMID:22210458
ccPDB: compilation and creation of data sets from Protein Data Bank. PMID:22139939
The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations. PMID:22115427
Animal Toxins: How is Complexity Represented in Databases? PMID:22069583
MimoDB 2.0: a mimotope database and beyond. PMID:22053087
Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. PMID:22020785
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. PMID:22006843
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. PMID:21993301
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice. PMID:21936904
Structure of N5-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis. PMID:21931218
Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae. PMID:21870198
Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures. PMID:21842229
Mechanism for noncompetitive inhibition by novel GluN2C/D N-methyl-D-aspartate receptor subunit-selective modulators. PMID:21807990
A model of calcium activation of the cardiac thin filament. PMID:21797264
Atomic structure of bacteriophage Sf6 tail needle knob. PMID:21705802
Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain. PMID:21636896
Characterization of the structure and function of Klebsiella pneumoniae allantoin racemase. PMID:21616082
Crystal structure of human natural cytotoxicity receptor NKp30 and identification of its ligand binding site. PMID:21444796
Structural analysis of a novel class of R-M controller proteins: C.Csp231I from Citrobacter sp. RFL231. PMID:21440553
Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal. PMID:21383919
Biochemical mechanism of pathogenesis of human gonadotropin-releasing hormone receptor mutants Thr104Ile and Tyr108Cys associated with familial hypogonadotropic hypogonadism. PMID:21277937
Identification of novel conserved functional motifs across most Influenza A viral strains. PMID:21272360
Protein structure databases. PMID:21225378
1,000 structures and more from the MCSG. PMID:21219649
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. PMID:21177659
Identification and characterization of a bacterial glutamic peptidase. PMID:21122090
MimoDB: a new repository for mimotope data derived from phage display technology. PMID:21079566
Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. PMID:21070951
Structure of dihydroorotase from Bacillus anthracis at 2.6 Å resolution. PMID:21045288
PDBe: Protein Data Bank in Europe. PMID:21045060
Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger. PMID:20944230
The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes. PMID:20944228
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism. PMID:20944224
Crystal structure of human interferon-λ1 in complex with its high-affinity receptor interferon-λR1. PMID:20934432
Shared paramyxoviral glycoprotein architecture is adapted for diverse attachment strategies. PMID:20863312
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. PMID:20796320
The CoFactor database: organic cofactors in enzyme catalysis. PMID:20679331
Bioinformatic Identification of Novel Methyltransferases. PMID:20582239
Protein annotation and modelling servers at University College London. PMID:20507913
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
The molecular evolution of PL10 homologs. PMID:20438638
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. PMID:20368334
SAROTUP: scanner and reporter of target-unrelated peptides. PMID:20339521
Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PMID:20231898
Crystal structure of the nonerythroid alpha-spectrin tetramerization site reveals differences between erythroid and nonerythroid spectrin tetramer formation. PMID:20228407
Fast and efficient searching of biological data resources--using EB-eye. PMID:20150321
Mechanisms responsible for a PhiX174 mutant's ability to infect Escherichia coli by phosphorylation. PMID:20147402
The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603). PMID:20054114
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
PTGL: a database for secondary structure-based protein topologies. PMID:19906706
PDBe: Protein Data Bank in Europe. PMID:19858099
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position. PMID:19625641
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families. PMID:19594936
RASMOT-3D PRO: a 3D motif search webserver. PMID:19417073
PDBsum additions PubMed citations: 138.

138 articles citing: PDBsum additions

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins. PMID:35794124
Cytoskeletal regulation of a transcription factor by DNA mimicry via coiled-coil interactions. PMID:35725768
PDBsum extras: SARS-CoV-2 and AlphaFold models. PMID:34779073
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions. PMID:34361778
Metabolic Adaptations to Marine Environments: Molecular Diversity and Evolution of Ovothiol Biosynthesis in Bacteria. PMID:34272861
PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. PMID:33950214
Structure of trypanosome coat protein VSGsur and function in suramin resistance. PMID:33462435
Rational Drug Design for Pseudomonas aeruginosa PqsA Enzyme: An in silico Guided Study to Block Biofilm Formation. PMID:33195420
The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases. PMID:32754173
Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatis. PMID:32751237
Characterizing the Fused TvG6PD::6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP+ Molecule on Enzyme Stability. PMID:32650494
Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies. PMID:32060794
S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. PMID:32057875
Functional characterization and subcellular distribution of two recombinant cytosolic HSP70 isoforms from Entamoeba histolytica under normal and stress conditions. PMID:32056023
A Thermolabile Phospholipase B from Talaromyces marneffei GD-0079: Biochemical Characterization and Structure Dynamics Study. PMID:32033124
MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
Histone deposition promotes recombination-dependent replication at arrested forks. PMID:31584934
Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation. PMID:31533362
Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. PMID:31204053
Interplay between the Kinesin and Tubulin Mechanochemical Cycles Underlies Microtubule Tip Tracking by the Non-motile Ciliary Kinesin Kif7. PMID:31031197
Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. PMID:30984210
High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. PMID:30917325
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Crystal structure of E. coli PRPP synthetase. PMID:30646888
Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus. PMID:30402510
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PMID:30346968
CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii. PMID:30345257
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model. PMID:30257460
Two Tau binding sites on tubulin revealed by thiol-disulfide exchanges. PMID:30218010
Biochemical Characterization and Structural Modeling of Fused Glucose-6-Phosphate Dehydrogenase-Phosphogluconolactonase from Giardia lamblia. PMID:30149622
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. PMID:30034403
Crystal structure of an L chain optimised 14F7 anti-ganglioside Fv suggests a unique tumour-specificity through an unusual H-chain CDR3 architecture. PMID:30022069
In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51. PMID:29928016
The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host. PMID:29844443
SWISS-MODEL: homology modelling of protein structures and complexes. PMID:29788355
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Crystal structure of Brugia malayi venom allergen-like protein-1 (BmVAL-1), a vaccine candidate for lymphatic filariasis. PMID:29501266
Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family. PMID:29453256
Crystal structure of thermospermine synthase from Medicago truncatula and substrate discriminatory features of plant aminopropyltransferases. PMID:29367265
The structure of FIV reverse transcriptase and its implications for non-nucleoside inhibitor resistance. PMID:29364950
Prediction of Hot Spots at Myeloid Cell Leukemia-1-Inhibitor Interface Using Energy Estimation and Alanine Scanning Mutagenesis. PMID:29345906
Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet. PMID:29335428
A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells. PMID:29180448
Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. PMID:29144442
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Computational design of new protein kinase D 1 (PKD1) inhibitors: homology-based active site prediction, energy-optimized pharmacophore, docking and database screening. PMID:29058231
ChannelsDB: database of biomacromolecular tunnels and pores. PMID:29036719
Structure-Based Prototype Peptides Targeting the Pseudomonas aeruginosa Type VI Secretion System Effector as a Novel Antibacterial Strategy. PMID:28979890
First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target? PMID:28955968
Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA. PMID:28934476
PDBsum: Structural summaries of PDB entries. PMID:28875543
Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. PMID:28784764
Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface. PMID:28705932
Computational and Experimental Studies of ADP-Ribosylation. PMID:28695527
S-adenosyl-L-homocysteine hydrolase from a hyperthermophile (Thermotoga maritima) is expressed in Escherichia coli in inactive form - Biochemical and structural studies. PMID:28629859
Is the hydrophobic core a universal structural element in proteins? PMID:28623601
Structural Basis of Egg Coat-Sperm Recognition at Fertilization. PMID:28622512
Drug repurposing for aging research using model organisms. PMID:28620943
Structural Basis for Importin-α Binding of the Human Immunodeficiency Virus Tat. PMID:28490747
Whole-protein alanine-scanning mutagenesis of allostery: A large percentage of a protein can contribute to mechanism. PMID:28407397
Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. PMID:28373573
Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. PMID:28368281
Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c). PMID:28346784
A Newly Determined Member of the meso-Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum. PMID:28341677
Mutations in catalase-peroxidase KatG from isoniazid resistant Mycobacterium tuberculosis clinical isolates: insights from molecular dynamics simulations. PMID:28303436
Stilbene epoxidation and detoxification in a Photorhabdus luminescens-nematode symbiosis. PMID:28246174
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
Protein Bioinformatics Databases and Resources. PMID:28150231
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Computational Analysis of Damaging Single-Nucleotide Polymorphisms and Their Structural and Functional Impact on the Insulin Receptor. PMID:27840822
Sequence-Based Prediction of RNA-Binding Residues in Proteins. PMID:27787829
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. PMID:27763556
Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication. PMID:27642006
A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms. PMID:27633952
In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions. PMID:27559295
Key Residues for Catalytic Function and Metal Coordination in a Carotenoid Cleavage Dioxygenase. PMID:27453555
Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases. PMID:27423402
Structural Analysis of an Avr4 Effector Ortholog Offers Insight into Chitin Binding and Recognition by the Cf-4 Receptor. PMID:27401545
PDBparam: Online Resource for Computing Structural Parameters of Proteins. PMID:27330281
Catestatin Gly364Ser Variant Alters Systemic Blood Pressure and the Risk for Hypertension in Human Populations via Endothelial Nitric Oxide Pathway. PMID:27324226
Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation. PMID:27226615
Cyanidin inhibits quorum signalling pathway of a food borne opportunistic pathogen. PMID:27162376
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T. PMID:27129264
Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA. PMID:27105075
Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1). PMID:27083005
Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. PMID:27066023
Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. PMID:26994138
Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop. PMID:26929404
Insights into the mechanism of human papillomavirus E2-induced procaspase-8 activation and cell death. PMID:26906543
Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50. PMID:26896444
Expression and purification of an engineered, yeast-expressed Leishmania donovani nucleoside hydrolase with immunogenic properties. PMID:26839079
Dissecting protein architecture with communication blocks and communicating segment pairs. PMID:26823083
SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level. PMID:26819632
Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity. PMID:26796657
Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism. PMID:26776105
New crystal form of human ubiquitin in the presence of magnesium. PMID:26750481
Structural basis for PECAM-1 homophilic binding. PMID:26702061
The structure of Medicago truncatula δ(1)-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants. PMID:26579138
A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers. PMID:26556795
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. PMID:26538500
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. PMID:26471730
Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins. PMID:26465610
Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications. PMID:26462798
Gating machinery of InsP3R channels revealed by electron cryomicroscopy. PMID:26458101
A Functional EXXEK Motif is Essential for Proton Coupling and Active Glucosinolate Transport by NPF2.11. PMID:26443378
An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life. PMID:26434770
Comprehensive assessment of cancer missense mutation clustering in protein structures. PMID:26392535
A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis. PMID:26361768
Sequential unfolding of the hemolysin two-partner secretion domain from Proteus mirabilis. PMID:26350294
Phosphorylation at serine 52 and 635 does not alter the transport properties of glucosinolate transporter AtGTR1. PMID:26340317
Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding. PMID:26321039
Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae. PMID:26296208
Quercetin Influences Quorum Sensing in Food Borne Bacteria: In-Vitro and In-Silico Evidence. PMID:26248208
"PP2C7s", Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases. PMID:26241330
Molecular docking to explore the possible binding mode of potential inhibitors of thioredoxin glutathione reductase. PMID:26239395
Structural and Biochemical Characterization of the Francisella tularensis Pathogenicity Regulator, Macrophage Locus Protein A (MglA). PMID:26121147
PLIP: fully automated protein-ligand interaction profiler. PMID:25873628
Crystal structure of a two-subunit TrkA octameric gating ring assembly. PMID:25826626
Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins. PMID:25805991
A hypertrophic cardiomyopathy-associated MYBPC3 mutation common in populations of South Asian descent causes contractile dysfunction. PMID:25583989
Antibacterial drug leads: DNA and enzyme multitargeting. PMID:25574764
On the electrostatic properties of homodimeric proteins. PMID:25419028
A series of PDB-related databanks for everyday needs. PMID:25352545
EzCatDB: the enzyme reaction database, 2015 update. PMID:25324316
A molecular model of human Lysyl Oxidase (LOX) with optimal copper orientation in the catalytic cavity for induced fit docking studies with potential modulators. PMID:25187679
The Protein Data Bank archive as an open data resource. PMID:25062767
Prediction and redesign of protein-protein interactions. PMID:24878423
Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences. PMID:24776850
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding. PMID:24598754
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579
http://dx.doi.org/10.1093/nar/gkt940

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molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: PDBsum; PDBsum; at-a-glance overview of macromolecular structures; DOI: https://doi.org/10.25504/FAIRsharing.7vjq5t; Last edited: Feb. 11, 2020, 8:24 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein structure analysis
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