ArticleStructure (London, England : 1993)2017
Validation of Structures in the Protein Data Bank.
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Article in Structure (London, England : 1993), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers.
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163citing papers in PubMed
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163 citing papers in PubMed.
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- A cryptic allosteric pocket shapes isoform-selective inhibition of human malic enzymes.Protein science : a publication of the Protein Society · 2026Article
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- Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution.Acta crystallographica. Section D, Structural biology · 2026Article
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- Functional divergence and structural changes of Class IV histone deacetylases (HDACs) across the tree of life.Molecular biology and evolution · 2026Article
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- Structural insights into the antibacterial function of the Pseudomonas putida effector Tke5.The EMBO journal · 2026Article
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Functional divergence of two soybean cytosolic serine hydroxymethyltransferases in development and defense against soybean cyst nematode.Frontiers in plant science · 2026Article
- A survey of crystallographic quality metrics from CIFs in the Cambridge Structural Database.IUCrJ · 2025Article
- Halogen bonds between ligands and proteins: Can we use them in validation?Protein science : a publication of the Protein Society · 2025Article
- Interplay between malic enzyme 2, de novo serine synthesis, and the malate-aspartate shuttle drives metabolic adaptation in triple-negative breast cancer.Cancer & metabolism · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps.Acta crystallographica. Section D, Structural biology · 2025Article
103 more citing papers are in PubMed but not listed here.
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Authors and funding
34 authors.
Swanand GoreProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Eduardo Sanz GarcíaProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Pieter M S HendrickxProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Aleksandras GutmanasProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address: gutmanas@ebi.ac.uk.
John D WestbrookRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Huanwang YangRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Zukang FengRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Kumaran BaskaranBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
John M BerrisfordProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Brian P HudsonRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Yasuyo IkegawaPDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Naohiro KobayashiPDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Catherine L LawsonRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Steve MadingBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Lora MakProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Abhik MukhopadhyayProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Thomas J OldfieldProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ardan PatwardhanProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Ezra PeisachRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Gaurav SahniProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Monica R SekharanRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Sanchayita SenProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Chenghua ShaoRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Oliver S SmartProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Eldon L UlrichBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Reiko YamashitaPDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Martha QuesadaRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Jasmine Y YoungRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Haruki NakamuraPDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
John L MarkleyBMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA.
Helen M BermanRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Stephen K BurleyRCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA.
Sameer VelankarProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Gerard J KleywegtProtein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Funding
Unified Data Resource for Large Complexes Determined by Cryo-Electron MicroscopyR01GM079429 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2007 to 2021
$11.6MThe BMRB as an evolving resource for biomolecular structure-function researchR01GM109046 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI HOCH, JEFFREY C · 2014 to 2022
$6.6MBiotechnology and Biological Sciences Research Council BB/G022577/1Biotechnology and Biological Sciences Research Council BB/J007471/1Biotechnology and Biological Sciences Research Council BB/K016970/1Biotechnology and Biological Sciences Research Council BB/K020013/1Biotechnology and Biological Sciences Research Council BB/M011674/1Biotechnology and Biological Sciences Research Council BB/M013146/1Biotechnology and Biological Sciences Research Council BB/M020347/1Biotechnology and Biological Sciences Research Council BB/M020428/1Medical Research Council MR/L007835/1NIGMS NIH HHS R01 GM079429NIGMS NIH HHS R01 GM109046Wellcome Trust 104948Wellcome Trust 75968Wellcome Trust 88944
Abstract
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.
Indexed as
Validation Studies as TopicDatabases, ProteinSequence Analysis, Protein3D macromolecular structurebiocurationdata archivingdata depositionPDBstructural biologystructure data qualityvalidationwwPDB
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.