RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Rose, Yana; Duarte, Jose M.; Lowe, Robert; Segura, Joan; Bi, Chunxiao; Bhikadiya, Charmi; Chen, Li; Rose, Alexander S.; Bittrich, Sebastian; Burley, Stephen K.; Westbrook, John D.

doi:10.1016/j.jmb.2020.11.003

Title: RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Journal Article · Sat May 01 00:00:00 EDT 2021 · Journal of Molecular Biology

DOI:https://doi.org/10.1016/j.jmb.2020.11.003· OSTI ID:1769487

Rose, Yana; Duarte, Jose M.; Lowe, Robert; Segura, Joan; Bi, Chunxiao; Bhikadiya, Charmi; Chen, Li; Rose, Alexander S.; Bittrich, Sebastian; Burley, Stephen K.; Westbrook, John D.

The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign of RCSB PDB data delivery services that build on existing PDBx/mmCIF data schemas. New data access APIs (data.rcsb.org) enable efficient delivery of all PDB archive data. A novel GraphQL-based API provides flexible, declarative data retrieval along with a simple-to-use REST API. A powerful new search system (search.rcsb.org) seamlessly integrates heterogeneous types of searches across the PDB archive. Searches may combine text attributes, protein or nucleic acid sequences, small-molecule chemical descriptors, 3D macromolecular shapes, and sequence motifs. The new RCSB.org architecture adheres to the FAIR Principles, empowering users to address a wide array of research problems in fundamental biology, biomedicine, biotechnology, bioengineering, and bioenergy.

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Research Organization:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); National Cancer Institute (NCI); National Institute of Allergy and Infectious Diseases (NIAID); National Institute of General Medical Science (NIGMS)

Grant/Contract Number:: SC0019749; DBI-1832184; R01GM133198

OSTI ID:: 1769487

Alternate ID(s):: OSTI ID: 1853378

Journal Information:: Journal of Molecular Biology, Journal Name: Journal of Molecular Biology Vol. 433 Journal Issue: 11; ISSN 0022-2836

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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