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Title: RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Abstract

Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designatedmore » Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [2];  [2];  [4];  [2];  [2]; ORCiD logo [3];  [5];  [2];  [2];  [2];  [6];  [2]; ORCiD logo [7];  [2];  [2];  [3] more »;  [2];  [3];  [2];  [2];  [2];  [2];  [2];  [2];  [3];  [6];  [3];  [2];  [2];  [2];  [2]; ORCiD logo [6]; ORCiD logo [2];  [2];  [2];  [6]; ORCiD logo [2] « less
+ Show Author Affiliations
  1. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Cancer Institute of New Jersey, Rutgers, The State University of New Jersey New Brunswick New Jersey USA, Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center, University of California La Jolla California USA, Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey Piscataway New Jersey USA
  2. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey USA
  3. Research Collaboratory for Structural Bioinformatics Protein Data Bank San Diego Supercomputer Center, University of California La Jolla California USA
  4. School of Chemistry and Materials Science Rochester Institute of Technology Rochester New York USA
  5. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Cancer Institute of New Jersey, Rutgers, The State University of New Jersey New Brunswick New Jersey USA
  6. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences Quantitative Biosciences Institute, University of California San Francisco California USA, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Pharmaceutical Chemistry Quantitative Biosciences Institute, University of California San Francisco California USA
  7. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Cancer Institute of New Jersey, Rutgers, The State University of New Jersey New Brunswick New Jersey USA, Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla California USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1984170
Alternate Identifier(s):
OSTI ID: 1906236
Grant/Contract Number:  
DE‐SC0019749
Resource Type:
Published Article
Journal Name:
Protein Science
Additional Journal Information:
Journal Name: Protein Science Journal Volume: 31 Journal Issue: 12; Journal ID: ISSN 0961-8368
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai J., Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Benjamin, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, and Zardecki, Christine. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. United Kingdom: N. p., 2022. Web. doi:10.1002/pro.4482.
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Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai J., Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Benjamin, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, & Zardecki, Christine. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. United Kingdom. https://doi.org/10.1002/pro.4482
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Burley, Stephen K., Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A., Crichlow, Gregg V., Dalenberg, Kenneth, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W., Ganesan, Sai J., Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P., Khokhriakov, Igor, Lawson, Catherine L., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W., Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Benjamin, Westbrook, John D., Whetstone, Shamara, Young, Jasmine Y., Zalevsky, Arthur, and Zardecki, Christine. Wed . "RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D". United Kingdom. https://doi.org/10.1002/pro.4482.
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@article{osti_1984170,
title = {RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D},
author = {Burley, Stephen K. and Bhikadiya, Charmi and Bi, Chunxiao and Bittrich, Sebastian and Chao, Henry and Chen, Li and Craig, Paul A. and Crichlow, Gregg V. and Dalenberg, Kenneth and Duarte, Jose M. and Dutta, Shuchismita and Fayazi, Maryam and Feng, Zukang and Flatt, Justin W. and Ganesan, Sai J. and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel Kramer and Guranovic, Vladimir and Henry, Jeremy and Hudson, Brian P. and Khokhriakov, Igor and Lawson, Catherine L. and Liang, Yuhe and Lowe, Robert and Peisach, Ezra and Persikova, Irina and Piehl, Dennis W. and Rose, Yana and Sali, Andrej and Segura, Joan and Sekharan, Monica and Shao, Chenghua and Vallat, Brinda and Voigt, Maria and Webb, Benjamin and Westbrook, John D. and Whetstone, Shamara and Young, Jasmine Y. and Zalevsky, Arthur and Zardecki, Christine},
abstractNote = {Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.},
doi = {10.1002/pro.4482},
journal = {Protein Science},
number = 12,
volume = 31,
place = {United Kingdom},
year = {Wed Nov 16 00:00:00 EST 2022},
month = {Wed Nov 16 00:00:00 EST 2022}
}
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  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn582

SAbDab: the structural antibody database
journal, November 2013

  • Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1043

SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database
journal, November 2018

  • Chandonia, John-Marc; Fox, Naomi K.; Brenner, Steven E.
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1134

Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells
journal, August 2017

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
journal, September 1998

  • Shindyalov, I. N.; Bourne, P. E.
  • Protein Engineering Design and Selection, Vol. 11, Issue 9
  • DOI: 10.1093/protein/11.9.739

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development
journal, January 2021

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density
journal, April 2017

  • Pearce, Nicholas M.; Krojer, Tobias; Bradley, Anthony R.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15123

Ligand Depot: a data warehouse for ligands bound to macromolecules
journal, April 2004

BioJava 5: A community driven open-source bioinformatics library
journal, February 2019

Chimeric Antigen Receptors
journal, October 2017

Transmembrane proteins in the Protein Data Bank: identification and classification
journal, June 2004

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions
journal, November 2018

  • Newport, Thomas D.; Sansom, Mark S. P.; Stansfeld, Phillip J.
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1047

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine
journal, October 2021

  • Zardecki, Christine; Dutta, Shuchismita; Goodsell, David S.
  • Protein Science, Vol. 31, Issue 1
  • DOI: 10.1002/pro.4200

Crystallography: Protein Data Bank
journal, October 1971

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19
journal, December 2021

  • Owen, Dafydd R.; Allerton, Charlotte M. N.; Anderson, Annaliesa S.
  • Science, Vol. 374, Issue 6575
  • DOI: 10.1126/science.abl4784

BioMagResBank
journal, December 2007

  • Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm957

IMGT®, the international ImMunoGeneTics information system® 25 years on
journal, November 2014

  • Lefranc, Marie-Paule; Giudicelli, Véronique; Duroux, Patrice
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1056

Validation of Structures in the Protein Data Bank
journal, December 2017

Discovery of Small-Molecule Inhibitors of the PD-1/PD-L1 Axis That Promote PD-L1 Internalization and Degradation
journal, February 2022

Human Papillomavirus and Vaccines
journal, May 2018

Impact of the Protein Data Bank on antineoplastic approvals
journal, May 2020

Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities
journal, July 2017

p53 Tumor Suppressor
journal, July 2002

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
journal, October 2021

  • Bekker, Gert‐Jan; Yokochi, Masashi; Suzuki, Hirofumi
  • Protein Science, Vol. 31, Issue 1
  • DOI: 10.1002/pro.4211

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
journal, December 2019

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
journal, August 2019

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
journal, November 2021

  • Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao
  • Protein Science, Vol. 31, Issue 1
  • DOI: 10.1002/pro.4213

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
journal, January 2018

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
journal, September 1992

Ebola Virus Proteins
journal, October 2014

Responsible Data Science
journal, June 2017

  • van der Aalst, Wil M. P.; Bichler, Martin; Heinzl, Armin
  • Business & Information Systems Engineering, Vol. 59, Issue 5
  • DOI: 10.1007/s12599-017-0487-z

RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
journal, April 2005

  • Nederveen, Aart J.; Doreleijers, Jurgen F.; Vranken, Wim
  • Proteins: Structure, Function, and Bioinformatics, Vol. 59, Issue 4
  • DOI: 10.1002/prot.20408

Cisplatin and DNA
journal, March 2021

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
journal, October 2022

  • Burley, Stephen K.; Berman, Helen M.; Duarte, Jose M.
  • Biomolecules, Vol. 12, Issue 10
  • DOI: 10.3390/biom12101425
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