PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

John D Westbrook; Jasmine Y Young; Chenghua Shao; Zukang Feng; Vladimir Guranovic; Catherine L Lawson; Brinda Vallat; Paul D Adams; John M Berrisford; Gerard Bricogne; Kay Diederichs; Robbie P Joosten; Peter Keller; Nigel W Moriarty; Oleg V Sobolev; Sameer Velankar; Clemens Vonrhein; David G Waterman; Genji Kurisu; Helen M Berman; Stephen K Burley; Ezra Peisach

doi:10.1016/j.jmb.2022.167599

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

J Mol Biol. 2022 Jun 15;434(11):167599. doi: 10.1016/j.jmb.2022.167599. Epub 2022 Apr 20.

Authors

John D Westbrook¹, Jasmine Y Young², Chenghua Shao², Zukang Feng², Vladimir Guranovic², Catherine L Lawson², Brinda Vallat², Paul D Adams³, John M Berrisford⁴, Gerard Bricogne⁵, Kay Diederichs⁶, Robbie P Joosten⁷, Peter Keller⁵, Nigel W Moriarty⁸, Oleg V Sobolev⁸, Sameer Velankar⁴, Clemens Vonrhein⁵, David G Waterman⁹, Genji Kurisu¹⁰, Helen M Berman¹¹, Stephen K Burley¹², Ezra Peisach¹³

Affiliations

¹ 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.
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 Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA.
⁴ Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁵ Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK.
⁶ University of Konstanz, 78457 Konstanz, Germany.
⁷ Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands. Electronic address: https://www.twitter.com/Robbie_Joosten.
⁸ Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁹ UKRI-STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, UK; CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK. Electronic address: https://www.twitter.com/upintheair.
¹⁰ Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
¹¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; The Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.
¹² 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; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA. Electronic address: stephen.burley@rcsb.org.
¹³ 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. Electronic address: ezra.peisach@rcsb.org.

Abstract

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

Keywords: biological data; data management; data standard; macromolecular structure; protein data bank (PDB).

Publication types

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

MeSH terms

Computational Biology*
Crystallography*
Databases, Protein*
Macromolecular Substances / chemistry
Molecular Biology
Protein Conformation
Semantics
Software*

Substances

Macromolecular Substances

Abstract

Publication types

MeSH terms

Substances

Grants and funding