The Protein Data Bank archive as an open data resource

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

• Publication year

  2014

• Venue

  Journal of Computer-Aided Molecular Design

• Publication date

  2014-07-26

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1007/s10822-014-9770-yPMID 25062767PMCID 4196035
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• SCOP2 prototype: a new approach to protein structure mining

  2014cited by this paper
• A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits

  2014cited by this paper
• The future of the Protein Data Bank.

  2013cited by this paper
• ArchDB 2014: structural classification of loops in proteins

  2013cited by this paper
• Recommendations of the wwPDB NMR Validation Task Force.

  2013cited by this paper
• 3did: a catalog of domain-based interactions of known three-dimensional structure

  2013cited by this paper
• PDBe: Protein Data Bank in Europe

  2013cited by this paper
• SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

  2013cited by this paper
• PDBsum additions

  2013cited by this paper
• PDBTM: Protein Data Bank of transmembrane proteins after 8 years

  2012cited by this paper
• Protein data bank

  2012cited by this paper
• Outcome of the First Electron Microscopy Validation Task Force Meeting

  2012cited by this paper
• Implementing an X-ray validation pipeline for the Protein Data Bank

  2012cited by this paper
• Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

  2011cited by this paper
• The wwPDB common tool for deposition and annotation

  2011cited by this paper
• ChEMBL: a large-scale bioactivity database for drug discovery

  2011cited by this paper
• A New Generation of Crystallographic Validation Tools for the Protein Data Bank

  2011cited by this paper
• Safeguarding the integrity of protein archive

  2010cited by this paper
• EMDataBank.org: unified data resource for CryoEM

  2010cited by this paper
• Extending CATH: increasing coverage of the protein structure universe and linking structure with function

  2010cited by this paper
• DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs

  2010cited by this paper
• BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

  2008cited by this paper
• The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery.

  2008cited by this paper
• The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies

  2008cited by this paper
• BioMagResBank

  2007cited by this paper
• International Tables for Crystallography: Definition and exchange of crystallographic data

  2006cited by this paper
• BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities

  2006cited by this paper
• J. D. Bernal: The Sage of Science

  2006cited by this paper
• Binding MOAD (Mother Of All Databases)

  2005cited by this paper
• The PDBbind database: methodologies and updates.

  2005cited by this paper
• Definition and exchange of crystallographic data

  2005cited by this paper
• Cold Spring Harbor Symposia on Quantitative Biology

  2005cited by this paper
• PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

  2004cited by this paper
• SCOP database in 2004: refinements integrate structure and sequence family data

  2004cited by this paper
• Announcing the worldwide Protein Data Bank

  2003cited by this paper
• International tables for crystallography

  2002cited by this paper
• Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution

  2000cited by this paper
• Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.

  2000cited by this paper
• Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

  2000cited by this paper
• The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

  2000cited by this paper
• The Protein Data Bank

  2000cited by this paper
• The protein data bank

  1999cited by this paper
• Refined structure of an intact IgG2a monoclonal antibody.

  1997cited by this paper
• Crystal structure of the nucleosome core particle at 2.8 Å resolution

  1997cited by this paper
• The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

  1997cited by this paper
• Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.

  1996cited by this paper
• Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA target

  1992cited by this paper
• Between objectivity and subjectivity

  1990cited by this paper
• Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00.

  1989cited by this paper
• The missing crystallography data.

  1989cited by this paper
• Crystal structure of trp represser/operator complex at atomic resolution

  1988cited by this paper
• The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure.

  1988cited by this paper
• Crystal structure of trp represser/operator complex at atomic resolution

  1988cited by this paper
• Proteins

  1987cited by this paper
• Biopolymers

  1984cited by this paper
• The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors

  1983cited by this paper
• X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature.

  1982cited by this paper
• Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement.

  1978cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper
• Structure of insulin in 4-zinc insulin

  1976cited by this paper
• CRYSNET, a crystallographic computing network with interactive graphics display.

  1974cited by this paper
• Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution.

  1972cited by this paper
• The crystal structure of insulin. 3. Evidence for a 2-fold axis in rhombohedral zinc insulin.

  1966cited by this paper
• Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis.

  1960cited by this paper
• Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis

  1960cited by this paper
• Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution

  1960cited by this paper
• A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis

  1958cited by this paper
• International union of crystallography

  1953cited by this paper
• X-Ray Photographs of Crystalline Pepsin

  1934cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis

  2026cites this paper
• A fully automated benchmarking suite to compare macromolecular complexes

  2025cites this paper
• Advancing Drug Repurposing for Rheumatoid Arthritis: Integrating Protein–Protein Interaction, Molecular Docking, and Dynamics Simulations for Targeted Therapeutic Approaches

  2025cites this paper
• Expression and interaction of RNA binding protein HuR with multidrug transporters (P-GP, MRP1, and ABCG2) in chemoresistant breast and colorectal cancer cells

  2025cites this paper
• Molecular Docking and Simulation Analysis of Glioblastoma Cell Surface Receptors and Their Ligands: Identification of Inhibitory Drugs Targeting Fibronectin Ligand to Potentially Halt Glioblastoma Pathogenesis

  2025cites this paper
• In silico repurposing of FDA-approved drugs against MEK1: structural and dynamic insights into lung cancer therapeutics

  2025cites this paper
• Microbial Enhancement of Plant Tolerance to Waterlogging: Mechanisms and Interplay with Biological Control of Pathogens

  2025cites this paper
• Superbug Neisseria gonorrhoeae Infections: The Role of the Moonlighting Protein Glutamate Racemase in Treatment and Prevention.

  2025cites this paper
• Essential database resources for modern drug discovery.

  2025cites this paper
• Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

  2025cites this paper
• RCSB Protein Data Bank: revolutionising drug discovery and design for over five decades

  2025influential citation
• Supporting the CIF file format of proteins in molecular dynamics simulations

  2024cites this paper
• Anthelmintic and analgesic activities of different solvent fractions of crude methanolic extract of Baccaurea ramiflora (Lour.) fruit peels and seeds with molecular docking analysis

  2024cites this paper
• Network Pharmacological Analysis of Hydroxychloroquine Intervention in the Treatment of Iga Nephropathy

  2024cites this paper
• Advances in AI for Protein Structure Prediction: Implications for Cancer Drug Discovery and Development

  2024cites this paper
• Standardizing macromolecular structure files: further efforts are needed.

  2023cites this paper
• Breaking Barriers: Workshop on Open Data Practices in AutoUI Research

  2023cites this paper
• Ten recommendations for organising bioimaging data for archival

  2023cites this paper
• lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

  2023cites this paper
• Supporting CIF Format of Biomolecular Structures in GROMACS

  2023cites this paper
• Computational Investigation of Functional Water Molecules Upon GPCR Bound to G protein or Arrestin

  2022cites this paper
• 1 General Information 1 . 1 Name of the consortium

  2022cites this paper
• Improved compound–protein interaction site and binding affinity prediction using self-supervised protein embeddings

  2022cites this paper
• Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin

  2022cites this paper
• Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps

  2022cites this paper
• PDBms—An online tool for PDB file splitting and interactive molecular visualization

  2022cites this paper
• PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

  2022cites this paper
• Discovery of Immunomodulators from Plant Kingdom Targeting IL-6 for the Effective Management Therapy of SARS-CoV-2

  2022cites this paper
• Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor

  2022cites this paper
• Computational Repurposing Model of Curcumin as a Drug

  2021cites this paper
• Interaction energy between neuronal cell receptors and peptoid ligands.

  2021cites this paper
• ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

  2021cites this paper
• A Unique Approach to Treat Rheumatic Heart Disease by Using In Silico Modeling With Polymeric Nanoparticles

  2021cites this paper
• Drug Repurposing: In Silico Modeling of Streptococcus Infection

  2021cites this paper
• PDBeCIF: an open-source mmCIF/CIF parsing and processing package

  2021cites this paper
• International Journal of Scientific Research in Science and Technology

  2021cites this paper
• The Opportunities and Challenges of Research Data and Software for Libraries and Institutional Repositories

  2021cites this paper
• Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations.

  2020influential citation
• Expansin Engineering Database: A navigation and classification tool for expansins and homologues

  2020cites this paper
• Conformational analysis of a cyclic AKH neuropeptide analog that elicits selective activity on locust versus honeybee receptor.

  2020cites this paper
• A Novel Network Pharmacology Strategy to Decode Metabolic Biomarkers and Targets Interactions for Depression

  2020cites this paper
• A Multiscale Model to Predict Neuronal Cell Deformation with Varying Extracellular Matrix Stiffness and Topography

  2020cites this paper
• Estimating the Effect of Single-Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein

  2020cites this paper
• Phote-HrTH (Phormia terraenovae Hypertrehalosaemic Hormone), the Metabolic Hormone of the Fruit Fly: Solution Structure and Receptor Binding Model

  2020cites this paper
• Network Pharmacology Based Prediction of Active Ingredients and Targets of Chinese Herb She Xiang in Treating Facial Paralysis 

  2020cites this paper
• A LOGICAL AND ONTOLOGICAL FRAMEWORK FOR KNOWLEDGE DISCOVERY ON GENE REGULATORY NETWORKS. CASE STUDY: BILE ACID AND XENOBIOTIC SYSTEM (BAXS)

  2020cites this paper
• Targeting a conserved pocket (n-octyl-β-D–glucoside) on the dengue virus envelope protein by small bioactive molecule inhibitors

  2020influential citation
• An Educational Bioinformatics Project to Improve Genome Annotation

  2020cites this paper
• BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

  2020cites this paper
• An integrated exploration of pharmacological potencies of Bischofia javanica (Blume) leaves through experimental and computational modeling

  2020cites this paper
• Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin‐α7 mediated nuclear import pathway

  2019cites this paper
• Biological Database Searching

  2019cites this paper
• Brazilian malaria molecular targets (BraMMT): selected receptors for virtual high-throughput screening experiments

  2019cites this paper
• Protein Structure Databases

  2019cites this paper
• Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces

  2019cites this paper
• Screening of potential GCMS derived antimigraine compound from the leaves of Abrus precatorius Linn to target “calcitonin gene related peptide” receptor using in silico analysis

  2019cites this paper
• Quality Management for Big 3D Data Analytics: A Case Study of Protein Data Bank

  2019cites this paper
• Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease

  2019influential citation
• Identification and Analysis of Long Repeats of Proteins at the Domain Level

  2019influential citation
• Open-Access Activity Prediction Tools for Natural Products. Case Study: hERG Blockers.

  2019cites this paper
• The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years

  2019cites this paper
• MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

  2019cites this paper
• 3D Printing in the Context of Science, Technology, Engineering, and Mathematics Education at the College/University Level

  2019cites this paper
• Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

  2018cites this paper
• Towards Generalized Noise-Level Dependent Crystallographic Symmetry Classifications of More or Less Periodic Crystal Patterns

  2018cites this paper
• Bioinformatics

  2018cites this paper
• Marine Bacterial Compounds Evaluated by In Silico Studies as Antipsychotic Drugs Against Schizophrenia

  2018cites this paper
• A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells

  2018influential citation
• Modeling and Deorphanization of Orphan GPCRs.

  2018cites this paper
• Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway

  2018cites this paper
• All-atom molecular dynamics comparison of disease-associated zinc fingers

  2018cites this paper
• D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures.

  2018cites this paper
• Structural effects of point mutations in proteins

  2018cites this paper
• Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors

  2018influential citation
• Identification of Adjacent NNRTI Binding Pocket in Multi-mutated HIV1- RT Enzyme Model: An in silico Study.

  2018cites this paper
• Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

  2018cites this paper
• Structural biology data archiving – where we are and what lies ahead

  2018cites this paper
• CryoEM-based hybrid modeling approaches for structure determination.

  2018cites this paper
• Preparing 3D Print Files for Nano-Tech/Science Education from Entries of Large Open-Access Crystallographic Databases at Dedicated Websites

  2018cites this paper
• A Network Pharmacology-Based Approach to Investigate the Novel TCM Formula against Huntington's Disease and Validated by Support Vector Machine Model

  2018cites this paper
• Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

  2018cites this paper
• Homology-based loop modeling yields more complete crystallographic protein structures

  2018cites this paper
• Synchrotron Big Data Science.

  2018cites this paper
• Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads.

  2017cites this paper
• SEL120-34A is a novel CDK8 inhibitor active in AML cells with high levels of serine phosphorylation of STAT1 and STAT5 transactivation domains

  2017cites this paper
• Whaddaya Know: A Guide to Uncertainty and Subjectivity in Structural Biology.

  2017cites this paper
• New active leads for tuberculosis booster drugs by structure-based drug discovery.

  2017cites this paper
• 1.15 – Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space

  2017cites this paper
• The ProFunc Function Prediction Server.

  2017cites this paper
• Synthesis, SAR, and Docking Studies Disclose 2-Arylfuran-1,4-naphthoquinones as In Vitro Antiplasmodial Hits

  2017cites this paper
• Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes

  2017cites this paper
• Molecular characterization of haemophilia B patients in southern Brazil

  2017cites this paper
• Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data

  2017influential citation
• Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets

  2017cites this paper
• In Silico Structure Based Designing of Dihydrofolate Reductase Enzyme Antagonists and Potential Small Molecules That Target DHFR Protein to Inhibit the Folic Acid Biosynthetic Pathways

  2017cites this paper
• A broad pH range and processive chitinase from a metagenome library

  2017cites this paper
• Statin and rottlerin small-molecule inhibitors restrict colon cancer progression and metastasis via MACC1

  2017cites this paper
• Characterizing the Hot Spots Involved in RON-MSPβ Complex Formation Using In Silico Alanine Scanning Mutagenesis and Molecular Dynamics Simulation

  2017cites this paper
• OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

  2017cites this paper
• Chemoinformatische Datenintegration zur Analyse und Vorhersage von Interaktionen von kleinen organischen Molekülen mit deren Biomolekülen (Chemoinformatic data integration to analyse and predict drug-target interactions)

  2017cites this paper