RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

S.K. Burley(Rutgers, The State University of New Jersey), Charmi Bhikadiya(San Diego Supercomputer Center), Chunxiao Bi(San Diego Supercomputer Center), Sebastian Bittrich(San Diego Supercomputer Center), Henry Chao(Rutgers, The State University of New Jersey), Li Chen(Rutgers, The State University of New Jersey), P. Craig(Rochester Institute of Technology), G.V. Crichlow(Rutgers, The State University of New Jersey), Kenneth Dalenberg(Rutgers, The State University of New Jersey), José M. Duarte(San Diego Supercomputer Center), Shuchismita Dutta(Rutgers, The State University of New Jersey), Maryam Fayazi(Rutgers, The State University of New Jersey), Zukang Feng(Rutgers, The State University of New Jersey), Justin W. Flatt(Rutgers, The State University of New Jersey), Sai J. Ganesan(QB3), Sutapa Ghosh(Rutgers, The State University of New Jersey), David S. Goodsell(Rutgers, The State University of New Jersey), Rachel Kramer Green(Rutgers, The State University of New Jersey), Vladimir Guranović(Rutgers, The State University of New Jersey), Jeremy Henry(San Diego Supercomputer Center), Brian P. Hudson(Rutgers, The State University of New Jersey), Igor Khokhriakov(San Diego Supercomputer Center), Catherine L. Lawson(Rutgers, The State University of New Jersey), Yu‐He Liang(Rutgers, The State University of New Jersey), Robert Lowe(Rutgers, The State University of New Jersey), Ezra Peisach(Rutgers, The State University of New Jersey), Irina Persikova(Rutgers, The State University of New Jersey), Dennis W. Piehl(Rutgers, The State University of New Jersey), Yana Rose(San Diego Supercomputer Center), Andrej Šali(QB3), Joan Segura(San Diego Supercomputer Center), Monica Sekharan(Rutgers, The State University of New Jersey), Chenghua Shao(Rutgers, The State University of New Jersey), Brinda Vallat(Rutgers, The State University of New Jersey), Maria Voigt(Rutgers, The State University of New Jersey), Ben Webb(QB3), John Westbrook(Rutgers, The State University of New Jersey), Shamara Whetstone(Rutgers, The State University of New Jersey), Jasmine Young(Rutgers, The State University of New Jersey), Arthur O. Zalevsky(QB3), Christine Zardecki(Rutgers, The State University of New Jersey)
Nucleic Acids Research
November 24, 2022
10.1093/nar/gkac1077
Cited by 859Open Access
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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.

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