Publications

RCSB PDB resources and services are described in the journal articles and book chapters listed below and at .

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Information on citing the RCSB PDB and related resources is available.

2024

  • Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
    (2024) bioRxiv 2024.01.15.575520; doi: 10.1101/2024.01.15.575520

  • Community recommendations on cryoEM data archiving and validation
    (2024) IUCrJ 11: 140-151; doi: 10.1107/S2052252524001246

  • PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
    (2024) Database 2024: baae041 doi: 10.1093/database/baae041

  • RCSB Protein Data Bank: Exploring protein 3D similarities via comprehensive structural alignments
    (2024) Bioinformatics 40: btae370 doi: 10.1093/bioinformatics/btae370

  • Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
    (2024) Nat Methods 21: 1340–1348 doi: 10.1038/s41592-024-02321-7

  • ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration
    (2024) Bioinformatics Advances 4: vbae111 doi: 10.1093/bioadv/vbae111

  • IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods
    (2024) Journal of Molecular Biology 436: 168546 doi: 10.1016/j.jmb.2024.168546

  • Folding paper models of biostructures for outreach and education
    (2024) Patterns 5: 100931; doi: 10.1016/j.patter.2024.100931

  • RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures
    (2024) IUCrJ 11: 279-286; doi: 10.1107/S2052252524002604

  • Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
    (2024) Structure 32: 824-837.e1 doi: 10.1016/j.str.2024.02.011

  • Impact of structural biology and the Protein Data Bank on US FDA new drug approvals of low molecular weight antineoplastic agents 2019–2023
    (2024) Oncogene 43: 2229-2243 doi: 10.1038/s41388-024-03077-2

  • Describing and sharing molecular visualizations using the MolViewSpec toolkit
    (2024) Current Protocols 4: e1099. doi: 10.1002/cpz1.1099

  • Generative artificial intelligence performs rudimentary structural biology modeling
    (2024) Sci Rep 14: 19372 doi: 10.1038/s41598-024-69021-2

  • Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms
    (2024) J Microbiol Biol Educ. 25: e00019-24 doi: 10.1128/jmbe.00019-24

2023

  • RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
    (2023) Nucleic Acids Research 51: D488–D508 doi: 10.1093/nar/gkac1077

  • A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic
    (2023) bioRxiv doi: 10.1101/2023.01.30.526101

  • An idea to explore: How an interdisciplinary undergraduate course exploring a global health challenge in molecular detail enabled science communication and collaboration in diverse audiences
    (2023) BAMBed 51:137-145 doi: 10.1002/bmb.21699

  • Integrative visualization of the molecular structure of a cellular microdomain
    (2023) Protein Science 32:e4577 doi: 10.1002/pro.4577

  • RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances
    (2023) Journal of Molecular Biology 435: 167994 doi: 10.1016/j.jmb.2023.167994

  • ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models
    (2023) Journal of Molecular Biology 435: 168021 doi: 10.1016/j.jmb.2023.168021

  • Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership
    (2023) Acta Cryst. D79 792-795 doi: 10.1107/S2059798323006381

  • RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins
    (2023) Front. Bioinform. 3:1311287 doi: 10.3389/fbinf.2023.1311287

  • NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank
    (2023) bioRxiv doi: 10.1101/2023.10.24.563739

  • Community recommendations on cryoEM data archiving and validation
    (2023) arXiv doi: 10.48550/arXiv.2311.17640

  • The next decade in structural biology (2023) Structure 31: 1284-1288 doi: 10.1016/j.str.2023.10.002

  • Changing Aesthetics in Biomolecular Graphics
    (2023) IEEE Comput Graph Appl 43:94-101 doi: 10.1109/MCG.2023.3250680

2022

Image on the cover of the journal containing the article (2022) Structure 30: P55-68.e2 doi: 10.1016/j.str.2021.10.008 Image on the cover of the journal containing the article (2022) Structure 30: 252-262.e4 doi: 10.1016/j.str.2021.10.003 Image on the cover of the journal containing the article (2022) Bioinformatics 38: 1452–1454 doi: 10.1093/bioinformatics Image on the cover of the journal containing the article (2022) Proteins 90: 1054-1080 doi: 10.1002/prot.26250 Image on the cover of the journal containing the article (2022) Molecular Biology and Evolution 39: msac091 doi: 10.1093/molbev/msac091 Image on the cover of the journal containing the article (2022) Journal of Molecular Biology 434: 167599 doi: 10.1016/j.jmb.2022.167599 Image on the cover of the journal containing the article (2022) Bioinformatics 38:3304–3305 doi: 10.1093/bioinformatics/btac317 Image on the cover of the journal containing the article (2022) Journal of Integrative Bioinformatics 19: 20220013 doi: 10.1515/jib-2022-0013 Image on the cover of the journal containing the article (2022) Emerg Top Life Sci </em> 6: 231–243 doi: 10.1042/ETLS20210267 Image on the cover of the journal containing the article (2022) Oncogene </em> 41: 4333–4335 doi: 10.1038/s41388-022-02424-5 Image on the cover of the journal containing the article (2022) Structure 30: 1385-1394.e3 doi: 10.1016/j.str.2022.08.004 Image on the cover of the journal containing the article (2022) QRB Discovery 3: 1–10 doi: 10.1017/qrd.2022.10 Image on the cover of the journal containing the article (2022) Protein Science 31: e4482 doi: 10.1002/pro.4482 Image on the cover of the journal containing the article (2022) Biophys Rev 14: 1281–1301 doi: 10.1007/s12551-022-01013-w

  • PDB-101: Educational resources supporting molecular explorations through biology and medicine
    (2022) Protein Science 31: 129-140 doi: 10.1002/pro.4200

  • RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
    (2022) Protein Science 31: 187-208 doi: 10.1002/pro.4213

  • RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens
    (2022) Structure 30: P55-68.e2 doi: 10.1016/j.str.2021.10.008

  • Simplified quality assessment for small-molecule ligands in the Protein Data Bank
    (2022) Structure 30: 252-262.e4 doi: 10.1016/j.str.2021.10.003

  • RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
    (2022) Bioinformatics 38: 1452-1454 doi: 10.1093/bioinformatics/btab813

  • Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic
    (2022) Proteins 90: 1054-1080 doi: 10.1002/prot.26250

  • Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection
    (2022) Molecular Biology and Evolution 39: msac091 doi: 10.1093/molbev/msac091

  • PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
    (2022) Journal of Molecular Biology 434: 167599 doi: 10.1016/j.jmb.2022.167599

  • RCSB Protein Data Bank 1D3D module: Displaying positional features on macromolecular assemblies
    (2022) Bioinformatics 38:3304–3305 doi: 10.1093/bioinformatics/btac317

  • Integrative illustration of a JCVI-syn3A minimal cell
    (2022) Journal of Integrative Bioinformatics 19: 20220013 doi: 10.1515/jib-2022-0013

  • Molecular explorations of cancer biology and therapeutics at PDB-101
    (2022) Oncogene 41: 4333–4335 doi: 10.1038/s41388-022-02424-5

  • Exploring protein symmetry at the RCSB Protein Data Bank
    (2022) Emerg Top Life Sci 6: 231–243 doi: 10.1042/ETLS20210267

  • Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level
    (2022) Structure 30: 1385-1394.e3 doi: 10.1016/j.str.2022.08.004

  • Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
    (2022) Biomolecules 12: 1425 doi: 10.3390/biom12101425

  • Integrative structural modelling and visualisation of a cellular organelle
    (2022) QRB Discovery 3: 1–10 doi: 10.1017/qrd.2022.10

  • RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D
    (2022) Protein Science 31: e4482 doi: 10.1002/pro.4482

  • Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
    (2022) Biophys Rev 14: 1281–1301 doi: 10.1007/s12551-022-01013-w

2021

  • RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
    (2021) Nucleic Acids Research 49: D437–D451 doi: 10.1093/nar/gkaa1038

  • Molecular storytelling for online structural biology outreach and education
    (2021) Structural Dynamics 8: 020401 doi: 10.1063/4.0000077

  • Painting a Portrait of SARS-CoV-2
    (2021) American Scientist 109: 88-93 doi: 10.1511/2021.109.2.88

  • Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank
    (2021) Structure 29: 393-400.e391 doi: 10.1016/j.str.2021.02.004

  • CellPAINT: Turnkey Illustration of Molecular Cell Biology
    (2021) Frontiers in Bioinformatics 1 doi: 10.3389/fbinf.2021.660936

  • Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development
    (2021) Journal of Biological Chemistry 296: 100559 doi: 10.1016/j.jbc.2021.100559

  • RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive
    (2021) Journal of Molecular Biology 443: 166704 doi: 10.1016/j.jmb.2020.11.003

  • Synergies between the Protein Data Bank and the community
    (2021) Nature Structural & Molecular Biology 28: 400–401 doi: 10.1038/s41594-021-00586-6

  • Art as a tool for science
    (2021) Nature Structural & Molecular Biology 28: 402–403 doi: 10.1038/s41594-021-00587-5

  • Seeing the PDB
    (2021) Journal of Biological Chemistry 296:100742 doi: 10.1016/j.jbc.2021.100742

  • Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction
    (2021) Structure 29: 515-520 doi: 10.1016/j.str.2021.04.010

  • Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
    (2021) Nucleic Acids Research 49: W431–W437 doi: 10.1093/nar/gkab314

  • Transactions from the 70th Annual Meeting of the American Crystallographic Association: Structural Science-New Ways to Teach the Next Generation
    (2021) Struct Dyn 8:040401 doi: 10.1063/4.0000125

  • Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain
    (2021) Proceedings of the National Academy of Sciences 118 (30) e21057391181 doi: 10.1073/pnas.2105739118

  • Modernized uniform representation of carbohydrate molecules in the Protein Data Bank
    (2021) Glycobiology 31: 1204–1218 doi: 10.1093/glycob/cwab039

  • wwPDB biocuration: on the front line of structural biology
    (2021) Nature Methods 18: 431–432 doi: 10.1038/s41592-021-01137-z

  • Predicting Proteome-Scale Protein Structure with Artificial Intelligence
    (2021) N Engl J Med 385: 2191-2194 doi: 10.1056/NEJMcibr2113027

  • Picturing science: using art and imagination to explore new worlds
    (2021) Biochem (Lond) 43: 32–38 doi: 10.1042/bio_2021_156

  • From integrative structural biology to cell biology
    (2021) Journal of Biological Chemistry 296: 100743 doi: 10.1016/j.jbc.2021.100743

  • The Protein Data Bank Archive
    (2021) Methods Mol Biol 2305:3-21 doi: 10.1007/978-1-0716-1406-8_1

  • JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality
    (2021) Science Advances 7: eabe4724 doi: 10.1126/sciadv.abe4724

2020

  • RCSB Protein Data Bank: Enabling biomedical research and drug discovery
    (2020) Protein Science 29: 52-65 doi: 10.1002/pro.3730

  • D3R grand challenge 4: Blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
    (2020) Journal of Computer-Aided Molecular Design 580: 99–119 doi: 10.1007/s10822-020-00289-y

  • How to help the free market fight coronavirus
    (2020) Nature 34: 167 doi: 10.1038/d41586-020-00888-7

  • Art and Science of the Cellular Mesoscale
    (2020) Trends in Biochemical Sciences 45: 472-483 doi: 10.1016/j.tibs.2020.02.010

  • The TRUST Principles for digital repositories
    (2020) Sci Data 7:144 doi: 10.1038/s41597-020-0486-7

  • Impact of the Protein Data Bank Across Scientific Disciplines
    (2020) Data Science Journal 19:1-14 doi: 10.5334/dsj-2020-025

  • Impact of the Protein Data Bank on antineoplastic approvals
    (2020) Drug Discovery Today 25:837-850 doi: 10.1016/j.drudis.2020.02.002

  • Insights from 20  years of the Molecule of the Month
    (2020) BAMBed 48: 350-355 doi: 10.1002/bmb.21360

  • Real time structural search of the Protein Data Bank
    (2020) PLoS Comput Biol 16: e1007970 doi: 10.1371/journal.pcbi.1007970

  • Integrative illustration for coronavirus outreach
    (2020) PLoS Biol 18: e3000815 doi: 10.1371/journal.pbio.3000815

  • Virtual Boot Camp: COVID-19 evolution and structural biology
    (2020) BAMBed 48:511–513 doi: 10.1002/bmb.21428

  • Real-time structural motif searching in proteins using an inverted index strategy
    (2020) bioRxiv doi: 10.1101/2020.09.11.293977

  • RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study
    (2020) Oncogene 39: 6623–6632 doi: 10.1038/s41388-020-01461-2

  • BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management
    (2020) PLOS Computational Biology 16: e1008247 doi: 10.1371/journal.pcbi.1008247

  • High-performance macromolecular data delivery and visualization for the web
    (2020) Acta Cryst D76: 1167-1173 doi: 10.1107/S2059798320014515

  • Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic
    (2020) bioRxiv 2020.12.01.406637 doi: 10.1101/2020.12.01.406637

  • Real-time structural motif searching in proteins using an inverted index strategy
    (2020) PLoS Comput Biol 16: e1008502 doi: 10.1371/journal.pcbi.1008502

  • RCSB Protein Data Bank 1D tools and services
    (2020) Bioinformatics 36: 5526-5527 doi: 10.1093/bioinformatics/btaa1012

2019

  • RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
    (2019) Nucleic Acids Research 47: D464–D474. doi: 10.1093/nar/gky1004

  • How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals
    (2019) Structure 27: 211-217 doi: 10.1016/j.str.2018.11.007

  • Protein Data Bank: the single global archive for 3D macromolecular structure data
    (2019) Nucleic Acids Research 47: D520–D528. doi: 10.1093/nar/gky949

  • BioJava 5: A community driven open-source bioinformatics library
    (2019) PLoS Comput Biol 15: e1006791. doi: 10.1371/journal.pcbi.1006791

  • Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
    (2019) Acta Crystallographica Section D 75: 451-454 doi: 10.1107/S2059798319004522

  • Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
    (2019) PLoS Comput Biol 15: e1006842 doi: 10.1371/journal.pcbi.1006842

  • Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
    (2019) Structure 27: 326-1335 doi: 10.1016/j.str.2019.05.012

  • Symmetry at the Cellular Mesoscale
    (2019) Symmetry 11: 1170 doi: 10.3390/sym11091170

  • Molecular Graphics: Bridging Structural Biologists and Computer Scientists
    (2019) Structure 75: 451-454 doi: 10.1016/j.str.2019.09.001

  • Illustrate: Software for Biomolecular Illustration
    (2019) Structure 27: 1617-1623-1720 doi: 10.1016/j.str.2019.08.011

  • Bringing Molecular Dynamics Simulation Data into View
    (2019) Trends Biochem Sci 44: 902-913 doi: 10.1016/j.tibs.2019.06.004

  • Assessment of protein assembly prediction in CASP13
    (2019) Proteins 87: 1190-1199 doi: 10.1002/prot.25795

  • Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
    (2019) Structure 27: 1745-1759 doi: 10.1016/j.str.2019.11.002

  • Virtual Exploration of Biomolecular Structure and Function
    (2019) in Biochemistry Education: From Theory to Practice 2T.J. Bussey, K. Linenberger Cortes, R.C. Austin (eds.) pp. 21-41 American Chemical Society doi: 10.1021/bk-2019-1337.ch002

  • Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences
    (2019) Proteins 87: 1298-1314 doi: 10.1002/prot.25827

2018

  • Investigation of protein quaternary structure via stoichiometry and symmetry ınformation
    (2018) PLoS ONE 13: e0197176. doi: 10.1371/journal.pone.0197176

  • RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education
    (2018) Protein Science 27: 316–330 doi: 10.1002/pro.3331

  • Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
    (2018) Database 2018: bay002 doi: 10.1093/database/bay002

  • Recon3D enables a three-dimensional view of gene variation in human metabolism
    (2018) Nature Biotechnology 36: 272–281 doi: 10.1038/nbt.4072

  • Automated evaluation of quaternary structures from protein crystals
    (2018) PLoS Comput Biol 14: e1006104 doi: 10.1371/journal.pcbi.1006104

  • Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach
    (2018) Scientific Data 5: 180293 doi: 10.1038/sdata.2018.293

  • Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm (2018) bioRxiv doi: 10.1101/297960

  • From atoms to cells: Using mesoscale landscapes to construct visual narratives
    (2018) Journal of Molecular Biology 430: 3954–3968 doi: 10.1016/j.jmb.2018.06.009

  • Molecular illustration in research and education: Past, present, and future
    (2018) Journal of Molecular Biology 430: 3969-3981 doi: 10.1016/j.jmb.2018.04.043

  • Learning biology through molecular storytelling
    (2018) The Science Teacher 86: 28-33

  • NGL viewer: web-based molecular graphics for large complexes
    (2018) Bioinformatics 34: 3755–3758. doi: 10.1093/bioinformatics/bty419

  • Analysis of impact metrics for the Protein Data Bank
    (2018) Scientific Data 5: 180212 doi: 10.1038/sdata.2018.212

  • Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank
    (2018) Biopolymers 109: e23230 doi: 10.1002/bip.23230

  • Mol*: Towards a common library and tools for web molecular graphics
    (2018) In Byska, J., Krone, M. and Sommer, B. (eds.), MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2018. The Eurographics Association. doi: 10.2312/molva.20181103

2017

  • The RCSB protein data bank: integrative view of protein, gene and 3D structural information
    (2017) Nucleic Acids Research 45: D271-D281 doi: 10.1093/nar/gkw1000

  • OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the Protein Data Bank (PDB) Archive
    (2017) Structure 25: 536-545 doi: 10.1016/j.str.2017.01.004

  • Multivariate Analyses of Quality Metrics for Crystal Structures in the Protein Data Bank Archive.
    (2017) Structure 25: 458-468 doi: 10.1016/j.str.2017.01.013

  • Data management: A global coalition to sustain core data
    (2017) Nature 543: 179 doi: 10.1038/543179a

  • Towards coordinated international support of core data resources for the life sciences
    (2017) bioRxiv doi: 10.1101/110825

  • Impact of genetic variation on three dimensional structure and function of proteins
    (2017) PLOS ONE 12(3): e0171355 doi: 10.1371/journal.pone.0171355

  • Towards an efficient compression of 3D coordinates of macromolecular structures
    (2017) PLOS ONE 12(3): e0174846 doi: 10.1371/journal.pone.0174846

  • MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures.
    (2017) bioRxiv doi: 10.1101/122689

  • BioJava-ModFinder: Identification of protein modifications in 3D structures from the Protein Data Bank
    (2017) Bioinformatics 33(13):2047-2049 doi: 10.1093/bioinformatics/btx101

  • Picturing Molecules at the RCSB Protein Data Bank
    (2017) SciArt Magazine June

  • Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive
    (2017) In Methods in Molecular Biology: Protein Crystallography Methods and Protocols (eds. A. Wlodawer, Z. Dauter, M. Jaskolski) Springer New York. 627-641 doi: 10.1007/978-1-4939-7000-1

  • MMTF--an efficient file format for the transmission, visualization, and analysis of macromolecular structures
    (2017) PLoS Comput Biol 13(6): e1005575. doi: 10.1371/journal.pcbi.1005575

  • PDB-Dev: A prototype system for depositing integrative / hybrid structural models
    (2017) Structure 25:1317-1318 doi: 10.1016/j.str.2017.08.001

  • Crystallography and Databases
    (2017) Data Science Journal 16:38 doi: 10.5334/dsj-2017-038

  • Assessment of protein assembly prediction in CASP12
    (2017) Proteins doi: 10.1002/prot.25408

  • Validation of the Structures in the Protein Data Bank
    (2017) Structure 25: 1916-1927 doi: 10.1016/j.str.2017.10.009

  • D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
    (2017) J Comput Aided Mol Des. doi: 10.1007/s10822-017-0088-4

  • NGLview - Interactive molecular graphics for Jupyter notebooks
    (2017) Bioinformatics btx789 doi: 10.1093/bioinformatics/btx789

  • MDsrv: viewing and sharing molecular dynamics simulations on the web
    (2017) Nat Methods 14:1123-1124 doi: 10.1038/nmeth.4497

  • Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
    (2017) Genome Med 9:113 doi: 10.1186/s13073-017-0509-y

2016

  • DCC: a Swiss army knife for structure factor analysis and validation
    (2016) Journal of Applied Crystallography 93:569-575 doi: 10.1107/S1600576716004428

  • Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
    (2016) Structure 24:502-508 doi: 10.1016/j.str.2016.02.017

  • Web-based molecular graphics for large complexes
    (2016) In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16). ACM, New York, NY, USA, 185-186. doi: 10.1145/2945292.2945324

  • Integrating Genomic Information with Protein Sequence and 3D Atomic Level Structure at the RCSB Protein Data Bank
    (2016) Bioinformatics 32 (24): 3833-3835 doi: 10.1093/bioinformatics/btw547

  • Specification of the Crystallographic Information File format, version 2.0
    (2016) Journal of Applied Crystallography 49: 277-284 doi: 10.1107/S1600576715021871

  • RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules
    (2016) Journal of Chemical Education 93:569-575 doi: 10.1021/acs.jchemed.5b00404

  • The archiving and dissemination of biological structure data
    (2016) Current Opinion in Structural Biology 40:17-22 doi: 10.1016/j.sbi.2016.06.018

  • Using the tools and resources of the RCSB Protein Data Bank
    (2016) Curr. Protoc. Bioinform. 55:1.9.1-1.9.35. doi: 10.1002/cpbi.13

2015

  • Citing a Data Repository: A Case Study of the Protein Data Bank
    (2015) PLoS ONE 10: e0136631 doi: 10.1371/journal.pone.0136631

  • Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
    (2015) Structure 23: 1156-1167 doi: 10.1016/j.str.2015.05.013

  • NMR Exchange Format: a unified and open standard for representation of NMR restraint data
    (2015) Nature Structural & Molecular Biology 22: 433-434 doi: 10.1038/nsmb.3041
  • The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology
    (2015) PLoS Biol 13(5): e1002140. doi: 10.1371/journal.pbio.1002140
  • Chapter 8 The Protein Data Bank: Overview and Tools for Drug Discovery
    (2015) Multifaceted Roles of Crystallography in Modern Drug Discovery, Series: NATO Science for Peace and Security Series A: Chemistry and Biology G. Scapin, D. Patel, E. Arnold, editors. Springer Science + Business Media Dordrecht, pp. 93-106 doi:10.1007/978-94-017-9719-1_8
  • The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
    (2015) Nucleic Acids Research 43(D1): D345-356 doi:10.1093/nar/gku1214
  • RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
    (2015) Bioinformatics 31: 126-127 doi:10.1093/bioinformatics/btu596

2014

  • Detection of Circular Permutations within Protein Structures using CE-C
    (2014) Bioinformatics doi:10.1093/bioinformatics/btu823
  • The Chemical Component Dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
    (2014) Bioinformatics doi:10.1093/bioinformatics/btu789
  • The Protein Data Bank archive as an open data resource
    (2014) Journal of Computer-Aided Molecular Design 28: 1009-1014 doi:10.1007/s10822-014-9770-y
  • Systematic Detection of Internal Symmetry in Proteins Using CE-Symm
    (2014) Journal of Molecular Biology 426: 2255-2268 doi:10.1016/j.jmb.2014.03.010
  • Small molecule annotation for the Protein Data Bank
    (2014) Database doi:10.1093/database/bau116
  • Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank
    (2014) Biopolymers 101:659-668 doi:10.1002/bip.22434
  • Establishing the Next Generation of the Protein Data Bank
    (2014) The Winnower doi:10.15200/winn.140076.68556
  • Response to On prompt update of literature references in the Protein Data Bank
    (2014) Acta Cryst D70: 2780 doi:10.1107/S1399004714020513

2013

  • The RCSB Protein Data Bank: new resources for research and education
    (2013) Nucleic Acids Research 41: D475-D482 doi:10.1093/nar/gks1200
  • Recommendations of the wwPDB NMR Validation Task Force
    (2013) Structure 21: 1563-1570 doi:10.1016/j.str.2013.07.021
  • How community has shaped the Protein Data Bank
    (2013) Structure 21: 1485-1491 doi:10.1016/j.str.2013.07.010
  • Revealing structural views of biology
    (2013) Biopolymers 99: 817-824 doi:10.1002/bip.22338
  • Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB Structure
    (2013) Structure 21: 875-881 doi:10.1016/j.str.2013.04.020
  • Trendspotting in the Protein Data Bank
    (2013) FEBS Lett. 587: 1036-45 doi:10.1016/j.febslet.2012.12.029
  • The Future of the Protein Data Bank
    (2013) Biopolymers 99: 218-222 doi:10.1002/bip.22132
  • Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al.
    (2013) Acta Cryst D69: 2296 doi:10.1107/S0907444913029168
  • Comment on On the propagation of errors by Jaskolski
    (2013) Acta Cryst D69: 2297 doi:10.1107/S090744491302917X
  • Chemical annotation of small and peptide-like molecules at the Protein Data Bank
    (2013) Database doi:10.1093/database/bat079
  • The Twists and Turns of DNA
    (2013) The Biologist 60: 18-22.

2012

  • Illustrating the Machinery of Life: Viruses
    (2012) Biochemistry and Molecular Biology Education 40: 291-296 doi:10.1002/bmb.20636
  • Putting proteins in context: scientific illustrations bring together information from diverse sources to provide an integrative view of the molecular biology of cells
    (2012) Bioessays 34(9):718-20 doi:10.1002/bies.201200072
  • Creating a community resource for protein science
    (2012) Protein Science 21: 1587-1596 doi:10.1002/pro.2154
  • BioJava: an open-source framework for bioinformatics in 2012
    (2012) Bioinformatics 28: 2693-2695 doi:10.1093/bioinformatics/bts494
  • Outcome of the first electron microscopy validation task force meeting
    (2012) Structure 20: 205-214 doi:10.1016/j.str.2011.12.014
  • The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future
    (2012) Structure 20: 391-396 doi:10.1016/j.str.2012.01.010
  • The Worldwide Protein Data Bank
    (2012) In International Tables for X-Ray Crystallography, Volume F: Crystallography of biological macromolecules
    E. Arnold, D. M. Himmel & M. G. Rossmann, editors Springer, Dordrecht, The Netherlands, pp. 827-832 doi:10.1107/97809553602060000111
  • Circular Permutation in Proteins
    (2012) PLoS Comput Bio 8: e1002445 doi:10.1371/journal.pcbi.1002445
  • The Protein Data Bank
    (2012) in Leadership in Science and Technology: A Reference Handbook, William Sims Bainbridge, editor SAGE Publications, Inc., Thousand Oaks, CA., volume 2, pages 661-675.

2011

  • The RCSB Protein Data Bank: redesigned web site and web services
    (2011) Nucleic Acids Res. 39: D392-D401 doi:10.1093/nar/gkq1021
  • Atomic evidence: the foundations of structural molecular biology
    (2011) Science Progress 94: 414-430 doi:10.3184/003685011X13201799666745
  • The evolution of the Protein Data Bank (part of special essay collection on the 40th anniversary of the PDB)
    (2011) Nature Structural & Molecular Biology 18: 1310 doi:10.1038/nsmb1211-1304
  • Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction
    (2011) Proteins: Structure, Function, and Bioinformatics 79: 6-20 doi:10.1002/prot.23196
  • A new generation of crystallographic validation tools for the Protein Data Bank
    (2011) Structure 19: 1395-1412 doi:10.1016/j.str.2011.08.006
  • Miniseries: Illustrating the machinery of life: Eukaryotic cell panorama
    (2011) Biochem Mol Biol Educ. 39:91-101 doi:10.1002/bmb.20494
  • The evolution of the RCSB Protein Data Bank website
    (2011) WIREs Computational Molecular Science 1: 782-789 doi:10.1002/wcms.57
  • The RCSB Protein Data Bank: site functionality and bioinformatics use cases
    (2011) NCI-Nature Pathway Interaction Database doi:10.1038/pid.2011.1
  • Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
    (2011) Database doi:10.1093/database/bar003

2010

  • dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment
    (2010) BMC Bioinformatics 11:310. doi:10.1186/1471-2105-11-310
  • Integration of open access literature into the RCSB Protein Data Bank Using BioLit
    (2010) BMC Bioinformatics 11:220. doi:10.1186/1471-2105-11-220
  • Will Widgets and Semantic Tagging Change Computational Biology?
    (2010) PLoS Comput Biol 6(2): e1000673. doi:10.1371/journal.pcbi.1000673

2009

  • Data Deposition and Annotation at the Worldwide Protein Data Bank
    (2009) Mol Biotechnol 42:1-13. doi: 10.1007/s12033-008-9127-7
  • The PDB format, mmCIF formats, and other data formats in Structural Bioinformatics, second edition
     (2009) Gu and Bourne, eds. John Wiley & Sons, Inc., Hoboken, NJ, pp 271-291
  • The Worldwide Protein Data Bank in Structural Bioinformatics, second edition
     (2009) Gu and Bourne, eds. John Wiley & Sons, Inc., Hoboken, NJ, pp 293-303.
  • Outcome of a Workshop on Applications of Protein Models in Biomedical Research
    (2009) Structure 17: 151-159. doi: 10.1016/j.str.2008.12.014

2008

  • Representation of viruses in the remediated PDB archive
    (2008) Acta Cryst. D64: 874-882 doi: 10.1107/S0907444908017393
  • Interesting Structures: Education and Outreach at the RCSB Protein Data Bank
    (2008) PLoS Biology 6:e117. doi: 10.1371/journal.pbio.0060117
  • Data deposition and annotation at the Worldwide Protein Data Bank
    (2008) Methods in Molecular Biology, vol. 426 doi: 10.1007/s12033-008-9127-7
  • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions
    (2008) J Biomol NMR 40(3): 153-155 doi: 10.1007/s10858-008-9221-y
  • Remediation of the Protein Data Bank archive
    (2008) Nucleic Acids Research 36: D426-433. doi: 10.1093/nar/gkm937
  • The Protein Data Bank: a historical perspective
    (2008) Acta Cryst. A64: 88-95. doi: 10.1107/S0108767307035623

2007

  • Using the Tools and Resources of the RCSB Protein Data Bank
    (2007) Current Protocols in Bioinformatics 1.9.1-1.9.24. doi: 10.1002/0471250953.bi0109s20
  • A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing
    (2007) Proteins 69(3): 449-65. doi: 10.1002/prot.21507
  • Realism about PDB
    (2007) Nature Biotechnology 25: 845-846. doi: 10.1038/nbt0807-845
  • The Research Collaboratory for Structural Bioinformatics Protein Data Bank
    (2007) Comprehensive Medicinal Chemistry II, Vol. 3, Drug Discovery Technologies, H. Kubinyi, Ed, Elsevier, Oxford, UK pp. 373-388.
  • The Worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    (2007) Nucleic Acids Res. 35(Database issue): D301-3. doi: 10.1093/nar/gkl971

2006

  • A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank
    (2006) PLoS Comput Biol 2(10): e99 doi: 10.1371/journal.pcbi.0020099
  • Archiving structural models of biological macromolecules: outcome of a workshop on biological macromolecular structure models
    (2006) Structure, 14: 1211-1217 doi: 10.1016/j.str.2006.06.005
  • Partitioning protein structures into domains: Why is it so difficult?
    (2006) J Mol Biol, 361(3): 562-90. doi: 10.1016/j.jmb.2006.05.060
  • Reflections on the science and law of structural biology, genomics, and drug development
    (2006) UCLA Law Review, 53: 871 - 908
  • The RCSB PDB information portal for structural genomics
    (2006) Nucleic Acids Research, Vol. 34, Database issue D302-D305 doi: 10.1093/nar/gkj120

2005

  • Using the Tools and Resources of the RCSB Protein Data Bank
    (2005) Current Protocols in Bioinformatics 1.9.1-1.9.40. doi: 10.1002/0471250953.bi0109s20
  • The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications
    (2005) BMC Bioinformatics, 6: 21. doi:10.1186/1471-2105-6-21
  • Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.
    (2005) PLoS Comp Biol 1(3): e31. doi:10.1371/journal.pcbi.0010031
  • PDBML: the representation of archival macromolecular structure data in XML
    (2005) Bioinformatics 21, pp. 988-992. doi: 10.1093/bioinformatics/bti082
  • Large Macromolecular Complexes in the Protein Data Bank: A Status Report
    (2005) Structure 13, pp. 381-388. doi:10.1016/j.str.2005.01.008
  • The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
    (2005) Nucl. Acids Res 33: D233-D237. doi:10.1093/nar/gki057
  • DDL2 dictionary, in International Tables for Crystallography
    (2005) J.D. Westbrook and S.R. Hall, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 473-481. doi:10.1107/97809553602060000750
  • The Macromolecular dictionary (mmCIF), in International Tables for Crystallography, Volume G
    (2005) P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 295-443. doi:10.1107/97809553602060000107
  • Classification and use of macromolecular data, in International Tables for Crystallography, Volume G
    (2005) P.M.D. Fitzgerald, J.D. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors., Springer: Dordrecht, The Netherlands. p. 144-198. doi:10.1107/97809553602060000107
  • Specification of a relational Dictionary Definition Language (DDL2), in International Tables for Crystallography, Volume G
    (2005) J.D. Westbrook, H.M. Berman, and S.R. Hall, , G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 61-72. doi:10.1107/97809553602060000107
  • The use of mmCIF architecture for PDB data management, in International Tables for Crystallography, Volume G
    (2005) J. Westbrook, H. Yang, Z. Feng, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors., Springer: Dordrecht, The Netherlands. p. 539-543. doi:10.1107/97809553602060000107
  • The Protein Data Bank exchange data dictionary, in International Tables for Crystallography, Volume G
    (2005) J. Westbrook, K. Henrick, E.L. Ulrich, and H.M. Berman, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 195-198. doi:10.1107/97809553602060000107
  • Image dictionary (imgCIF), in International Tables for Crystallography, Volume G
    (2005) A.P. Hammersley, H.J. Bernstein, and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 444-459. doi:10.1107/97809553602060000107
  • Specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
    (2005) S.R. Hall and J.D. Westbrook, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 20-36. doi:10.1107/97809553602060000107
  • Formal specification of the Crystallographic Information File, in International Tables for Crystallography, Volume G
    (2005) S.R. Hall, N. Spadaccini, I.D. Brown, H.J. Bernstein, J.D. Westbrook, and B. McMahon, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 25-36. doi:10.1107/97809553602060000107

2004

  • TargetDB: a target registration database for structural genomics projects
    (2004) Bioinformatics 20, pp. 2860-2862. doi: 10.1093/bioinformatics/bth300
  • Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
    (2004) Acta Cryst. D60, pp. 1833-1839. doi: 10.1107/S0907444904019419
  • Ligand Depot: a data warehouse for ligands bound to macromolecules
    (2004) Bioinformatics 20, pp. 2153-2155. doi: 10.1093/bioinformatics/bth214
  • The distribution and query systems of the RCSB Protein Data Bank
    (2004) Nucleic Acids Research, 32, pp. D223-5. doi: 10.1093/nar/gkh096
  • The Impact of Structural Genomics on the Protein Data Bank
    (2004) Am. J. PharmacoGenomics 4, pp. 247-252.
  • The Protein Data Bank and lessons in data management
    (2004) Briefings in Bioinformatics 5, pp 23-30. doi: 10.1093/bib/5.1.23
  • The PDB: A case study in management of community data
    (2004) Published in the inaugural issue of Current Proteomics. Current Proteomics 1, pp. 49-57. doi: 10.2174/1570164043488252

2003

  • Validation of protein structures for the PDB
    (2003) Methods Enzymol. 374, pp. 370-85. doi: 10.1016/S0076-6879(03)74017-8
  • Announcing the worldwide Protein Data Bank
    (2003) Nature Structural Biology, 10 (12), p. 980. doi: 10.1038/nsb1203-980
  • The PDB format, mmCIF formats and other data formats.
    (2003) P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc. pp. 161-179. 10.1038/80734
  • The Protein Data Bank and structural genomics
    (2003) Nucleic Acids Research 31, pp. 489-491. doi: 10.1093/nar/gkg068
  • The Protein Data Bank
    (2003) P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc. pp. 181-198.

2002

  • An ontology driven architecture for derived representations of macromolecular structure
    (2002) Bioinformatics 18 (9), pp. 1280-1281. Oxford University Press. doi: 10.1093/bioinformatics/18.9.1280
  • The CCPN project: an interim report on a data model for the NMR community
    (2002) Nature Structural Biology 9 (6), pp. 416-418. doi: 10.1038/nsb0602-416
  • Protein Structures: From Famine to Feast
    (2002) American Scientist 90 (4), pp. 350 - 359. doi: 10.1511/2002.4.350

2001

  • The Protein Data Bank, 2001 -
    (2001) In International Tables for Crystallography (M. G. Rossman & E. Arnold, eds.), Vol. F. Crystallography of Biological Macromolecules, pp. 675-662. Kluwer Academic Publishers, Dordrecht.
  • The PDB data uniformity project
    (2001) Nucleic Acids Research, 29: 214-218. doi: 10.1093/nar/29.1.214

2000

  • The Protein Data Bank and the challenge of structural genomics
    (2000) Nature Structural Biology, 7 (11), pp. 957-959. doi: 10.1038/80734