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. BurleyDepartment of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USACharmi BhikadiyaResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USAChunxiao BiResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USASebastian BittrichResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USAHenry ChaoInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USALi ChenInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAP. CraigSchool of Chemistry and Materials Science, Rochester Institute of Technology , Rochester , NY 14623, USAG.V. CrichlowInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAKenneth DalenbergInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAJosé M. DuarteResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USAShuchismita DuttaInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAMaryam FayaziInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAZukang FengInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAJustin W. FlattInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USASai J. GanesanResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco , San Francisco , CA 94158, USASutapa GhoshInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USADavid S. GoodsellDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla , CA 92037, USARachel Kramer GreenInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAVladimir GuranovićInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAJeremy HenryResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USABrian P. HudsonInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAIgor KhokhriakovResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USACatherine L. LawsonInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAYu‐He LiangInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USARobert LoweInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAEzra PeisachInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAIrina PersikovaInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USADennis W. PiehlInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAYana RoseResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USAAndrej ŠaliResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco , San Francisco , CA 94158, USAJoan SeguraResearch Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego , La Jolla , CA 92093, USAMonica SekharanInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAChenghua ShaoInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USABrinda VallatInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAMaria VoigtInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USABen WebbResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco , San Francisco , CA 94158, USAJohn WestbrookInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAShamara WhetstoneInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAJasmine YoungInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USAArthur O. ZalevskyResearch Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco , San Francisco , CA 94158, USAChristine ZardeckiInstitute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway , NJ 08854, USA
2022en
ABI
Аннотация
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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