RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600,000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, and 3D electron microscopy. PDB Data Consumers include researchers, educators, and students studying Fundamental Biology, Biomedicine, Biotechnology, and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past two years to RCSB PDB web portals in support of a ‘Structural View of Biology.’
- Authors:
-
more »
- Rutgers Univ., Piscataway, NJ (United States); Univ. of California, San Diego, CA (United States); Rutgers Univ., New Brunswick, NJ (United States)
- Rutgers Univ., Piscataway, NJ (United States)
- Univ. of California, San Diego, CA (United States)
- Rutgers Univ., Piscataway, NJ (United States); The Scripps Research Inst., La Jolla, CA (United States)
- Univ. of California, San Diego, CA (United States); ResMed, San Diego, CA (United States)
- Univ. of California, San Diego, CA (United States); Movemedical, San Diego, CA (United States)
- Rutgers Univ., Piscataway, NJ (United States); Comcast, Philadelphia, PA (United States)
- Publication Date:
- Research Org.:
- Rutgers Univ., New Brunswick, NJ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1600525
- Grant/Contract Number:
- SC0019749; DBI-1338415
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 47; Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Di Costanzo, Luigi, Christie, Cole, Dalenberg, Ken, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel K., Guranović, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Kalro, Tara, Liang, Yuhe, Lowe, Robert, Namkoong, Harry, Peisach, Ezra, Periskova, Irina, Prlić, Andreas, Randle, Chris, Rose, Alexander, Rose, Peter, Sala, Raul, Sekharan, Monica, Shao, Chenghua, Tan, Lihua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Woo, Jesse, Yang, Huanwang, Young, Jasmine, Zhuravleva, Marina, and Zardecki, Christine. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. United States: N. p., 2018.
Web. doi:10.1093/nar/gky1004.
Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Di Costanzo, Luigi, Christie, Cole, Dalenberg, Ken, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel K., Guranović, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Kalro, Tara, Liang, Yuhe, Lowe, Robert, Namkoong, Harry, Peisach, Ezra, Periskova, Irina, Prlić, Andreas, Randle, Chris, Rose, Alexander, Rose, Peter, Sala, Raul, Sekharan, Monica, Shao, Chenghua, Tan, Lihua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Woo, Jesse, Yang, Huanwang, Young, Jasmine, Zhuravleva, Marina, & Zardecki, Christine. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. United States. https://doi.org/10.1093/nar/gky1004
Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Di Costanzo, Luigi, Christie, Cole, Dalenberg, Ken, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel K., Guranović, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Kalro, Tara, Liang, Yuhe, Lowe, Robert, Namkoong, Harry, Peisach, Ezra, Periskova, Irina, Prlić, Andreas, Randle, Chris, Rose, Alexander, Rose, Peter, Sala, Raul, Sekharan, Monica, Shao, Chenghua, Tan, Lihua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Woo, Jesse, Yang, Huanwang, Young, Jasmine, Zhuravleva, Marina, and Zardecki, Christine. Wed .
"RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy". United States. https://doi.org/10.1093/nar/gky1004. https://www.osti.gov/servlets/purl/1600525.
@article{osti_1600525,
title = {RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy},
author = {Burley, Stephen K. and Berman, Helen M. and Bhikadiya, Charmi and Bi, Chunxiao and Chen, Li and Di Costanzo, Luigi and Christie, Cole and Dalenberg, Ken and Duarte, Jose M. and Dutta, Shuchismita and Feng, Zukang and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel K. and Guranović, Vladimir and Guzenko, Dmytro and Hudson, Brian P. and Kalro, Tara and Liang, Yuhe and Lowe, Robert and Namkoong, Harry and Peisach, Ezra and Periskova, Irina and Prlić, Andreas and Randle, Chris and Rose, Alexander and Rose, Peter and Sala, Raul and Sekharan, Monica and Shao, Chenghua and Tan, Lihua and Tao, Yi-Ping and Valasatava, Yana and Voigt, Maria and Westbrook, John and Woo, Jesse and Yang, Huanwang and Young, Jasmine and Zhuravleva, Marina and Zardecki, Christine},
abstractNote = {The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600,000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, and 3D electron microscopy. PDB Data Consumers include researchers, educators, and students studying Fundamental Biology, Biomedicine, Biotechnology, and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past two years to RCSB PDB web portals in support of a ‘Structural View of Biology.’},
doi = {10.1093/nar/gky1004},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United States},
year = {Wed Oct 24 00:00:00 EDT 2018},
month = {Wed Oct 24 00:00:00 EDT 2018}
}
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Structural biology: Gaining atomic level insight into the biological function of macromolecules
journal, November 2019
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- Experimental Biology and Medicine, Vol. 244, Issue 17
A bioinformatics investigation into the pharmacological mechanisms of the effect of the Yinchenhao decoction on hepatitis C based on network pharmacology
journal, February 2020
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Genome-wide mutation analysis of Helicobacter pylori after inoculation to Mongolian gerbils
journal, September 2019
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Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities
journal, December 2019
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Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon
journal, October 2019
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Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures
journal, October 2019
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Application of the SwissDrugDesign Online Resources in Virtual Screening
journal, September 2019
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- International Journal of Molecular Sciences, Vol. 20, Issue 18
Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets
journal, January 2020
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Integrated Computational Approaches and Tools for Allosteric Drug Discovery
journal, January 2020
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Marine Natural Products from Microalgae: An -Omics Overview
journal, May 2019
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Synthesis, Properties and Antimicrobial Activity of 5-Trifluoromethyl-2-formylphenylboronic Acid
journal, February 2020
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- Molecules, Vol. 25, Issue 4
A Comprehensive Cheminformatics Analysis of Structural Features Affecting the Binding Activity of Fullerene Derivatives
journal, January 2020
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VARIDT 1.0: variability of drug transporter database
journal, September 2019
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Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography
journal, April 2019
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Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
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ProCarbDB: A Database of Carbohydrate-binding Proteins
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Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
journal, January 2018
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Prediction of Liquid-Liquid Phase Separation Proteins Using Machine Learning
journal, January 2020
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Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography
journal, April 2019
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Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
journal, August 2019
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3D Electron Diffraction: The Nanocrystallography Revolution
journal, July 2019
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Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations
journal, January 2020
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Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method
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3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations
journal, February 2019
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The human DEPhOsphorylation Database DEPOD: 2019 update
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Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families
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Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning
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Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage
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VARIDT 1.0: variability of drug transporter database
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Genus for biomolecules
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ProCarbDB: a database of carbohydrate-binding proteins
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A bioinformatics investigation into the pharmacological mechanisms of the effect of the Yinchenhao decoction on hepatitis C based on network pharmacology
journal, February 2020
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- BMC Complementary Medicine and Therapies, Vol. 20, Issue 1
Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities
journal, December 2019
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- PLOS ONE, Vol. 14, Issue 12
Prediction of Liquid-Liquid Phase Separation Proteins Using Machine Learning
journal, January 2020
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A Review of Deep Learning Methods for Antibodies
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Uncovering the Pharmacological Mechanism of Stemazole in the Treatment of Neurodegenerative Diseases Based on a Network Pharmacology Approach
journal, January 2020
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Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets
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- International Journal of Molecular Sciences, Vol. 21, Issue 2
Marine Natural Products from Microalgae: An -Omics Overview
journal, May 2019
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pdbmine: A Node.js API for the RCSB Protein Data Bank (PDB)
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Fold combinations in multi-domain proteins
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Discovery of potential targets of Triptolide through inverse docking in ovarian cancer cells
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