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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Bhikadiya, Charmi (4)
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Bittrich, Sebastian ; Bhikadiya, Charmi ; Bi, Chunxiao ; Chao, Henry ; Duarte, Jose M. ; Dutta, Shuchismita ; Fayazi, Maryam ; Henry, Jeremy ; Khokhriakov, Igor ; Lowe, Robert ; et al ( , Journal of Molecular Biology)
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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. ; et al ( , Protein Science)
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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. ; et al ( , Nucleic Acids Research)
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.