Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

(2022) Daniel J Rigden et al.   NUCLEIC ACIDS RESEARCH

Simplified quality assessment for small-molecule ligands in the Protein Data Bank

(2022) Chenghua Shao et al.   STRUCTURE

Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor

(2022) Vasyl Bondarenko et al.   Nature Communications

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

(2022) John D. Westbrook et al.   JOURNAL OF MOLECULAR BIOLOGY

Ab initio phasing macromolecular structures using electron-counted MicroED data

(2022) Michael W. Martynowycz et al.   NATURE METHODS

Validation analysis of EMDB entries

(2022) Zhe Wang et al.   Acta Crystallographica Section D-Structural Biology

Molecular explorations of cancer biology and therapeutics at PDB-101

(2022) David S. Goodsell et al.   ONCOGENE

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

(2022) Shyamal Mosalaganti et al.   SCIENCE

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level

(2022) Chenghua Shao et al.   STRUCTURE

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

(2021) Zukang Feng et al.   STRUCTURE

Seeing the PDB

(2021) Jane S. Richardson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

From integrative structural biology to cell biology

(2021) Andrej Sali   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Genomics and the Protein Data Bank

(2021) Karolina Michalska et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

From structure to the dynamic regulation of a molecular switch: A journey over three decades

(2021) Susan S. Taylor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

50 Years of Structural Immunology

(2021) Ian A. Wilson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

How structural biology transformed studies of transcription regulation

(2021) Cynthia Wolberger   JOURNAL OF BIOLOGICAL CHEMISTRY

Cryo-electron tomography: observing the cell at the atomic level

(2021) Xueming Li   NATURE METHODS

RNA structure: a renaissance begins?

(2021) Rhiju Das   NATURE METHODS

Computational protein modeling and the next viral pandemic

(2021) Oleksandr Narykov et al.   NATURE METHODS

From structure to mechanism: skiing the energy landscape

(2021) Dorothee Kern   NATURE METHODS

A new era of synchrotron-enabled macromolecular crystallography

(2021) Aina E. Cohen   NATURE METHODS

Molecular visualization of cellular complexity

(2021) Michael R. Wozny et al.   NATURE METHODS

Expanding capabilities and infrastructure for cryo-EM

(2021) Kutti R. Vinothkumar   NATURE METHODS

Integrating experiments, theory and simulations into whole-cell models

(2021) Zaida Luthey-Schulten   NATURE METHODS

50 years of PDB: a catalyst in structural biology

(2021) Alexandre M. J. J. Bonvin   NATURE METHODS

Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction

(2021) Stephen K. Burley et al.   STRUCTURE

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP

(2021) Michael W. Martynowycz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Predicting Proteome-Scale Protein Structure with Artificial Intelligence

(2021) Stephen K. Burley et al.   NEW ENGLAND JOURNAL OF MEDICINE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Database resources of the national center for biotechnology information

(2021) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

(2021) Stephen K. Burley et al.   PROTEIN SCIENCE

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

(2021) Gert‐Jan Bekker et al.   PROTEIN SCIENCE

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

(2021) Christine Zardecki et al.   PROTEIN SCIENCE

Target highlights in CASP14 : Analysis of models by structure providers

(2021) Leila T. Alexander et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

New system for archiving integrative structures

(2021) Brinda Vallat et al.   Acta Crystallographica Section D-Structural Biology

Macromolecular movies, storybooks written by nature

(2021) Marius Schmidt   Biophysical Reviews

Impact of the Protein Data Bank on antineoplastic approvals

(2020) John D. Westbrook et al.   DRUG DISCOVERY TODAY

Pro‐islet amyloid polypeptide in micelles contains a helical prohormone segment

(2020) Charles F. DeLisle et al.   FEBS Journal

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Measurement of atom resolvability in cryo-EM maps with Q-scores

(2020) Grigore Pintilie et al.   NATURE METHODS

Integrative structure and function of the yeast exocyst complex

(2020) Sai J. Ganesan et al.   PROTEIN SCIENCE

Insights from 20 years of the Molecule of the Month

(2020) David S. Goodsell et al.   BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences

(2020) Issaku Yamada et al.   NATURE METHODS

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms

(2020) Nazar Mashtalir et al.   CELL

The promise and the challenges of cryo‐electron tomography

(2020) Martin Turk et al.   FEBS LETTERS

Atomic-resolution protein structure determination by cryo-EM

(2020) Ka Man Yip et al.   NATURE

Cryo-electron microscopy reaches atomic resolution

(2020) Mark A. Herzik Jr   NATURE

Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR

(2020) Manman Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Serial synchrotron crystallography for time-resolved structural biology

(2020) Arwen R Pearson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

The cryo-EM method microcrystal electron diffraction (MicroED)

(2019) Brent L. Nannenga et al.   NATURE METHODS

Advances in cryo-electron tomography and subtomogram averaging and classification

(2019) Peijun Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex

(2019) Diego F. Gauto et al.   Nature Communications

Thera-SAbDab: the Therapeutic Structural Antibody Database

(2019) Matthew I J Raybould et al.   NUCLEIC ACIDS RESEARCH

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

(2019) Jeffrey R. Wagner et al.   STRUCTURE

Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments

(2019) Robbins Puthenveetil et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PDBe: improved findability of macromolecular structure data in the PDB

(2019) David R Armstrong et al.   NUCLEIC ACIDS RESEARCH

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

(2019) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

SASBDB: Towards an automatically curated and validated repository for biological scattering data

(2019) Alexey G. Kikhney et al.   PROTEIN SCIENCE

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

(2019) Helen M. Berman et al.   STRUCTURE

Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography

(2018) Jose L. Olmos et al.   BMC BIOLOGY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

(2018) Brinda Vallat et al.   STRUCTURE

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

(2018) Jasmine Y Young et al.   Database-The Journal of Biological Databases and Curation

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

A call for public archives for biological image data

(2018) Jan Ellenberg et al.   NATURE METHODS

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database

(2018) John-Marc Chandonia et al.   NUCLEIC ACIDS RESEARCH

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

(2018) Thomas D Newport et al.   NUCLEIC ACIDS RESEARCH

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

(2018) Jose M Dana et al.   NUCLEIC ACIDS RESEARCH

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

(2018) John D. Westbrook et al.   STRUCTURE

Analysis of impact metrics for the Protein Data Bank

(2018) Christopher Markosian et al.   Scientific Data

GlyTouCan: an accessible glycan structure repository

(2017) Michael Tiemeyer et al.   GLYCOBIOLOGY

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

(2017) Stephen K. Burley et al.   PROTEIN SCIENCE

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

(2017) Jürgen Haas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

(2017) Jasmine Y. Young et al.   STRUCTURE

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

(2017) Chenghua Shao et al.   STRUCTURE

Validation of Structures in the Protein Data Bank

(2017) Swanand Gore et al.   STRUCTURE

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

(2017) Stephen K. Burley et al.   STRUCTURE

Engineering antibody therapeutics

(2016) Mark L Chiu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pharos: Collating protein information to shed light on the druggable genome

(2016) Dac-Trung Nguyen et al.   NUCLEIC ACIDS RESEARCH

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

(2016) Paul D. Adams et al.   STRUCTURE

The Cambridge Structural Database

(2016) Colin R. Groom et al.   Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

(2015) Aleksandras Gutmanas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PDBFlex: exploring flexibility in protein structures

(2015) Thomas Hrabe et al.   NUCLEIC ACIDS RESEARCH

EMDataBank unified data resource for 3DEM

(2015) Catherine L. Lawson et al.   NUCLEIC ACIDS RESEARCH

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

(2015) Omry Morag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manual classification strategies in the ECOD database

(2015) Hua Cheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

(2015) Andrej Sali et al.   STRUCTURE

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

(2015) Aleksandras Gutmanas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

(2014) Aqeel Ahmed et al.   NUCLEIC ACIDS RESEARCH

IMGT®, the international ImMunoGeneTics information system® 25 years on

(2014) Marie-Paule Lefranc et al.   NUCLEIC ACIDS RESEARCH

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

The Resolution Revolution

(2014) W. Kuhlbrandt   SCIENCE

Structure of catalase determined by MicroED

(2014) Brent L Nannenga et al.   eLife

OpenStructure: an integrated software framework for computational structural biology

(2013) M. Biasini et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The structure of the box C/D enzyme reveals regulation of RNA methylation

(2013) Audrone Lapinaite et al.   NATURE

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM

(2013) Xueming Li et al.   NATURE METHODS

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

ModBase, a database of annotated comparative protein structure models and associated resources

(2013) Ursula Pieper et al.   NUCLEIC ACIDS RESEARCH

Structural Dynamics and Topology of Phosphorylated Phospholamban Homopentamer Reveal Its Role in the Regulation of Calcium Transport

(2013) Vitaly V. Vostrikov et al.   STRUCTURE

Recommendations of the wwPDB NMR Validation Task Force

(2013) Gaetano T. Montelione et al.   STRUCTURE

The structure of the COPII transport-vesicle coat assembled on membranes

(2013) Giulia Zanetti et al.   eLife

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles

(2013) Xiao-chen Bai et al.   eLife

Collaboration gets the most out of software

(2013) Andrew Morin et al.   eLife

Three-dimensional electron crystallography of protein microcrystals

(2013) Dan Shi et al.   eLife

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Beam-induced motion of vitrified specimen on holey carbon film

(2012) Axel F. Brilot et al.   JOURNAL OF STRUCTURAL BIOLOGY

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

Femtosecond X-ray protein nanocrystallography

(2011) Henry N. Chapman et al.   NATURE

N-terminal domain of  B-crystallin provides a conformational switch for multimerization and structural heterogeneity

(2011) S. Jehle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

Dynamic Regulation of Archaeal Proteasome Gate Opening As Studied by TROSY NMR

(2010) T. L. Religa et al.   SCIENCE

ExplorEnz: the primary source of the IUBMB enzyme list

(2008) A. G. McDonald et al.   NUCLEIC ACIDS RESEARCH

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE