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

Burley, Stephen K.; Berman, Helen M.; Duarte, Jose M.; Feng, Zukang; Flatt, Justin W.; Hudson, Brian P.; Lowe, Robert; Peisach, Ezra; Piehl, Dennis W.; Rose, Yana; Sali, Andrej; Sekharan, Monica; Shao, Chenghua; Vallat, Brinda; Voigt, Maria; Westbrook, John D.; Young, Jasmine Y.; Zardecki, Christine

doi:10.3390/biom12101425

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

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of themore »« less

Authors:

; Berman, Helen M.;

; Feng, Zukang; Flatt, Justin W.; Hudson, Brian P.; Lowe, Robert; Peisach, Ezra; Piehl, Dennis W.; Rose, Yana; Sali, Andrej;

;

; Voigt, Maria; Westbrook, John D.; Young, Jasmine Y.;

Publication Date:: Tue Oct 04 00:00:00 EDT 2022

Sponsoring Org.:: USDOE

OSTI Identifier:: 1891545

Grant/Contract Number:: SC0019749

Resource Type:: Published Article

Journal Name:: Biomolecules

Additional Journal Information:: Journal Name: Biomolecules Journal Volume: 12 Journal Issue: 10; Journal ID: ISSN 2218-273X

Publisher:: MDPI AG

Country of Publication:: Switzerland

Language:: English

Citation Formats


                    Burley, Stephen K., Berman, Helen M., Duarte, Jose M., Feng, Zukang, Flatt, Justin W., Hudson, Brian P., Lowe, Robert, Peisach, Ezra, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., and Zardecki, Christine. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.  Switzerland: N. p., 2022. 
Web.  doi:10.3390/biom12101425.

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                    Burley, Stephen K., Berman, Helen M., Duarte, Jose M., Feng, Zukang, Flatt, Justin W., Hudson, Brian P., Lowe, Robert, Peisach, Ezra, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., & Zardecki, Christine. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.  Switzerland.  https://doi.org/10.3390/biom12101425

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                    Burley, Stephen K., Berman, Helen M., Duarte, Jose M., Feng, Zukang, Flatt, Justin W., Hudson, Brian P., Lowe, Robert, Peisach, Ezra, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Young, Jasmine Y., and Zardecki, Christine. Tue .  
"Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students".  Switzerland.  https://doi.org/10.3390/biom12101425.

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@article{osti_1891545,

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

  author       = {Burley, Stephen K. and Berman, Helen M. and Duarte, Jose M. and Feng, Zukang and Flatt, Justin W. and Hudson, Brian P. and Lowe, Robert and Peisach, Ezra and Piehl, Dennis W. and Rose, Yana and Sali, Andrej and Sekharan, Monica and Shao, Chenghua and Vallat, Brinda and Voigt, Maria and Westbrook, John D. and Young, Jasmine Y. and Zardecki, Christine},

  abstractNote = {The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.},

  doi          = {10.3390/biom12101425},

  journal      = {Biomolecules},

  number       = 10,

  volume       = 12,

  place        = {Switzerland},

  year         = {Tue Oct 04 00:00:00 EDT 2022},

  month        = {Tue Oct 04 00:00:00 EDT 2022}

}

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Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB‐designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three‐dimensional (3D) macromolecular structure data depositors (using macromolecularmore »« less
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Abstract

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Serial synchrotron crystallography for time-resolved structural biology journal, December 2020

Validation analysis of EMDB entries journal, April 2022

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy journal, June 1990

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The InterPro protein families and domains database: 20 years on journal, November 2020

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STAR/mmCIF: An ontology for macromolecular structure journal, February 2000

The ChEMBL database in 2017 journal, November 2016

From structure to mechanism: skiing the energy landscape journal, May 2021

Computational protein modeling and the next viral pandemic journal, May 2021

DrugBank 5.0: a major update to the DrugBank database for 2018 journal, November 2017

Dynamic Regulation of Archaeal Proteasome Gate Opening As Studied by TROSY NMR journal, April 2010

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection journal, December 2021

Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR journal, September 2020

Pro‐islet amyloid polypeptide in micelles contains a helical prohormone segment journal, March 2020

Macromolecular movies, storybooks written by nature journal, November 2021

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Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution journal, February 1960

The structure of the box C/D enzyme reveals regulation of RNA methylation journal, October 2013

50 years of PDB: a catalyst in structural biology journal, May 2021

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles journal, February 2013

Comparative Assessment of Scoring Functions: The CASF-2016 Update journal, November 2018

A protein structure from nuclear magnetic resonance data journal, March 1985

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing journal, March 1989

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology journal, June 2022

Database resources of the national center for biotechnology information journal, December 2021

The FAIR Guiding Principles for scientific data management and stewardship journal, March 2016

The molecular replacement method journal, February 1990

NMR Exchange Format: a unified and open standard for representation of NMR restraint data journal, June 2015

PDBe: improved findability of macromolecular structure data in the PDB journal, November 2019

Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry journal, March 1985

Serial femtosecond crystallography journal, August 2022

SWISS-MODEL: homology modelling of protein structures and complexes journal, May 2018

Integrative structure and functional anatomy of a nuclear pore complex
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Cryo-electron microscopy reaches atomic resolution
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Insights from 20 years of the Molecule of the Month
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Structural Dynamics and Topology of Phosphorylated Phospholamban Homopentamer Reveal Its Role in the Regulation of Calcium Transport
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The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope
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Impact of the Protein Data Bank Across Scientific Disciplines
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EMDataBank unified data resource for 3DEM
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Announcing the worldwide Protein Data Bank
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The Resolution Revolution
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Collaboration gets the most out of software
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The PRIDE database and related tools and resources in 2019: improving support for quantification data
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New electron microscopy database and deposition system
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The GTEx Consortium atlas of genetic regulatory effects across human tissues
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Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
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RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education: RCSB Protein Data Bank
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
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Femtosecond X-ray protein nanocrystallography
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Accurate prediction of protein structures and interactions using a three-track neural network
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Ab initio phasing macromolecular structures using electron-counted MicroED data
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Comparative Protein Structure Modeling Using MODELLER
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SASBDB: Towards an automatically curated and validated repository for biological scattering data
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Manual classification strategies in the ECOD database: ECOD Manual Classification Strategies
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Moving beyond static snapshots: Protein dynamics and the Protein Data Bank
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PubChem in 2021: new data content and improved web interfaces
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From structure to the dynamic regulation of a molecular switch: A journey over 3 decades
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50 Years of structural immunology
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Advances in cryo-electron tomography and subtomogram averaging and classification
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OpenStructure : an integrated software framework for computational structural biology
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Structural genomics and the Protein Data Bank
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Seeing the PDB
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Atomic-resolution protein structure determination by cryo-EM
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How structural biology transformed studies of transcription regulation
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The PDB and protein homeostasis: From chaperones to degradation and disaggregase machines
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From integrative structural biology to cell biology
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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
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Molecular visualization of cellular complexity
journal, May 2021

Analysis of impact metrics for the Protein Data Bank
journal, October 2018

Serial synchrotron crystallography for time-resolved structural biology
journal, December 2020

Validation analysis of EMDB entries
journal, April 2022

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
journal, June 1990

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

The promise and the challenges of cryo‐electron tomography
journal, October 2020

Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor
journal, February 2022

The InterPro protein families and domains database: 20 years on
journal, November 2020

Integrative structure and function of the yeast exocyst complex
journal, May 2020

Pharos: Collating protein information to shed light on the druggable genome
journal, November 2016

STAR/mmCIF: An ontology for macromolecular structure
journal, February 2000

The ChEMBL database in 2017
journal, November 2016

From structure to mechanism: skiing the energy landscape
journal, May 2021

Computational protein modeling and the next viral pandemic
journal, May 2021

DrugBank 5.0: a major update to the DrugBank database for 2018
journal, November 2017

Dynamic Regulation of Archaeal Proteasome Gate Opening As Studied by TROSY NMR
journal, April 2010

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection
journal, December 2021

Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR
journal, September 2020

Pro‐islet amyloid polypeptide in micelles contains a helical prohormone segment
journal, March 2020

Macromolecular movies, storybooks written by nature
journal, November 2021

Improved protein structure prediction using potentials from deep learning
journal, January 2020

A Bayesian View on Cryo-EM Structure Determination
journal, January 2012

UniProt: the universal protein knowledgebase in 2021
journal, November 2020

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level
journal, October 2022

Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution
journal, February 1960

The structure of the box C/D enzyme reveals regulation of RNA methylation
journal, October 2013

50 years of PDB: a catalyst in structural biology
journal, May 2021

Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles
journal, February 2013

Comparative Assessment of Scoring Functions: The CASF-2016 Update
journal, November 2018

A protein structure from nuclear magnetic resonance data
journal, March 1985

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing
journal, March 1989

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
journal, June 2022

Database resources of the national center for biotechnology information
journal, December 2021

The FAIR Guiding Principles for scientific data management and stewardship
journal, March 2016

The molecular replacement method
journal, February 1990

NMR Exchange Format: a unified and open standard for representation of NMR restraint data
journal, June 2015

PDBe: improved findability of macromolecular structure data in the PDB
journal, November 2019

Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry
journal, March 1985

Serial femtosecond crystallography
journal, August 2022

SWISS-MODEL: homology modelling of protein structures and complexes
journal, May 2018

RNA structure: a renaissance begins?
journal, May 2021

Protein structures from NMR
journal, July 1988

The Protein Data Bank
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