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

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

doi:10.1016/j.jmb.2020.11.003

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

J Mol Biol. 2021 May 28;433(11):166704. doi: 10.1016/j.jmb.2020.11.003. Epub 2020 Nov 10.

Authors

Affiliations

¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA.
² Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
³ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁴ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: [email protected].

Abstract

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.

Keywords: FAIR principles; computer architecture; databases; structural biology.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology*
Databases, Protein*
Macromolecular Substances / chemistry*
Search Engine*

Substances

Macromolecular Substances

Grants and funding

R01 GM133198/GM/NIGMS NIH HHS/United States