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. Issue Volume 51:Issue D1(2023) (24th November 2022)

• Record Type: Journal Article
• Authors: Burley, Stephen K; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chao, Henry; Chen, Li; Craig, Paul A; Crichlow, Gregg V; Dalenberg, Kenneth; Duarte, Jose M; Dutta, Shuchismita; Fayazi, Maryam; Feng, Zukang; Flatt, Justin W; Ganesan, Sai; Ghosh, Sutapa; Goodsell, David S; Green, Rachel Kramer; Guranovic, Vladimir; Henry, Jeremy; Hudson, Brian P; Khokhriakov, Igor; Lawson, Catherine L; Liang, Yuhe; Lowe, Robert; Peisach, Ezra; Persikova, Irina; Piehl, Dennis W; Rose, Yana; Sali, Andrej; Segura, Joan; Sekharan, Monica; Shao, Chenghua; Vallat, Brinda; Voigt, Maria; Webb, Ben; Westbrook, John D; Whetstone, Shamara; Young, Jasmine Y; Zalevsky, Arthur; Zardecki, Christine;
• Is Part Of: Nucleic acids research. Volume 51:Issue D1(2023)
• Page Start: D488
• Page End: D508
• Publication Date: 2022-11-24
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac1077
• Languages: English
• ISSNs: 0305-1048

Abstract

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. Graphical Abstract: