Publications

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

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

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

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

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

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

Investigation of protein quaternary structure via stoichiometry and symmetry ?nformation
(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

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

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

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