Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

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Publication Details

Journal
Nucleic Acids Research
Published
2024-11-28
DOI
https://doi.org/10.1093/nar/gkae1091
Citations
192
Primary Topic
Enzyme Structure and Function
Type
article
Field-Weighted Citation Impact
22.49

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article

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

Charmi Bhikadiya, Douglas Myers-Turnbull, Sutapa Ghosh, Ezra Peisach et al.
192 citations
Nucleic Acids Research
Enzyme Structure and Function
22.49
article

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

Charmi Bhikadiya, Douglas Myers-Turnbull, Sutapa Ghosh, Ezra Peisach, José M. Duarte, Jasmine Y. Young, Joan Segura, Alison Biester, Arthur O. Zalevsky, Justin W. Flatt, Igor Khokhriakov, Henry Chao, Brian P. Hudson, Catherine L. Lawson, Sebastian Bittrich, Tongji Xing, G.V. Crichlow, Andrej Săli, Jared Sagendorf, Vladimir Guranović, Chunxiao Bi, Shuchismita Dutta, David S. Goodsell, Brinda Vallat, Chenghua Shao, Irina Persikova, Yu‐He Liang, P. Craig, Yana Rose, Maria Voigt, Jhih‐Siang Lai, S.K. Burley, R K Bhatt, Prabuddha Biswas, Shamara Whetstone, Jeremy Henry, Monica R. Sekharan, Dennis W. Piehl, Rachel Kramer Green, Christine Zardecki, Jason T. Kaelber, James M. Smith, Ronald Brown, Amy Wu-Wu, Zukang Feng, Ben Webb, Mariya Joy, Santiago Blaumann, Vivek Reddy Chithari, Aditya Pingale, Michael Trumbull
article en
192 citations

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Nucleic Acids ResearchVol. 53(D1)
Rutgers, The State University of New Jersey (US), QB3 (US), Scripps Research Institute (US), Rochester Institute of Technology (US), University of California, San Francisco (US), San Diego Supercomputer Center (US)
National Science Foundation, U.S. Department of Energy, National Institutes of Health, Directorate for Biological Sciences, Biotechnology and Biological Sciences Research Council, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases
Climate action
Openalex Percentile: Top 0%
Enzyme Structure and Function
22.49
DOIOpen Access PDFOpenAlex
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