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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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Burley, Stephen K, Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chen, Li, Crichlow, Gregg V, Christie, Cole H, Dalenberg, Kenneth, Di Costanzo, Luigi, Duarte, Jose M, Dutta, Shuchismita, Feng, Zukang, Ganesan, Sai, Goodsell, David S, Ghosh, Sutapa, Green, Rachel Kramer, Guranović, Vladimir, Guzenko, Dmytro, Hudson, Brian P, Lawson, Catherine L, Liang, Yuhe, Lowe, Robert, Namkoong, Harry, Peisach, Ezra, Persikova, Irina, Randle, Chris, Rose, Alexander, Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Tao, Yi-Ping, Voigt, Maria, Westbrook, John D, Young, Jasmine Y, Zardecki, Christine, Zhuravleva, Marina·2021·Nucleic Acids Research

DOI 10.1093/nar/gkaa1038PMC PMC7779003

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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

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Authors: Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D. S., Ghosh, S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., Lawson, C. L., Liang, Y., Lowe, R., Namkoong, H., Peisach, E., Persikova, I., Randle, C., Rose, A., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Tao, Y.-P., Voigt, M., Westbrook, J. D., Young, J. Y., Zardecki, C., & Zhuravleva, M.
Affiliations: Rutgers, The State University of New Jersey (US)
San Diego Supercomputer Center (US)
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA
University of California, San Francisco (US)
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
Corresponding author: Burley, Stephen K
ORCID: Burley, Stephen K
Bhikadiya, Charmi
Bittrich, Sebastian
Chen, Li
Crichlow, Gregg V
Duarte, Jose M
Dutta, Shuchismita
Feng, Zukang
Ganesan, Sai
Goodsell, David S
Ghosh, Sutapa
Guranović, Vladimir
Guzenko, Dmytro
Hudson, Brian P
Lawson, Catherine L
Liang, Yuhe
Peisach, Ezra
Persikova, Irina
Rose, Alexander
Rose, Yana
Segura, Joan
Sekharan, Monica
Shao, Chenghua
Voigt, Maria
Westbrook, John D
Young, Jasmine Y
Zardecki, Christine
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2020-11-19
Volume: 49
Issue: D1
Pages: D437-D451
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkaa1038
PMC: PMC7779003
OpenAlex: W3104537585
Cited by: 1,581
References: 80
Citations by year: 2026: 188 · 2025: 196 · 2024: 272 · 2023: 352 · 2022: 374 · 2021: 194 · 2020: 3
FWCI: 91.93
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Nucleic Acids Research (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Rutgers University Community Repository (Rutgers University) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders: National Science Foundation (DBI-1832184)
U.S. Department of Energy (DE-SC0019749)
National Cancer Institute
National Institute of Allergy and Infectious Diseases
National Institute of General Medical Sciences (R01GM133198)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
Keywords: structural bioinformatics, Boolean search, SARS-CoV-2 proteins, COVID-19 pandemic, host cell proteins, macromolecular crystallography, NMR spectroscopy, 3D electron microscopy, micro-electron diffraction, structural biology education
MeSH terms: COVID-19, SARS-CoV-2, Biotechnology, Humans, Protein Conformation, Proteins, Software, Viral Proteins, Computational Biology, Databases, Protein, Biomedical Research, Macromolecular Substances, Bioengineering, Pandemics

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