ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

Brinda Vallat; Gerardo Tauriello; Stefan Bienert; Juergen Haas; Benjamin M Webb; Augustin Žídek; Wei Zheng; Ezra Peisach; Dennis W Piehl; Ivan Anischanka; Ian Sillitoe; James Tolchard; Mihaly Varadi; David Baker; Christine Orengo; Yang Zhang; Jeffrey C Hoch; Genji Kurisu; Ardan Patwardhan; Sameer Velankar; Stephen K Burley; Andrej Sali; Torsten Schwede; Helen M Berman; John D Westbrook

doi:10.1016/j.jmb.2023.168021

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

J Mol Biol. 2023 Jul 15;435(14):168021. doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23.

Authors

Brinda Vallat¹, Gerardo Tauriello², Stefan Bienert², Juergen Haas², Benjamin M Webb³, Augustin Žídek⁴, Wei Zheng⁵, Ezra Peisach⁶, Dennis W Piehl⁶, Ivan Anischanka⁷, Ian Sillitoe⁸, James Tolchard⁹, Mihaly Varadi⁹, David Baker¹⁰, Christine Orengo⁸, Yang Zhang⁵, Jeffrey C Hoch¹¹, Genji Kurisu¹², Ardan Patwardhan¹³, Sameer Velankar⁹, Stephen K Burley¹⁴, Andrej Sali¹⁵, Torsten Schwede², Helen M Berman¹⁶, John D Westbrook¹⁷

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. Electronic address: brinda.vallat@rcsb.org.
² Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
³ Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94157, USA.
⁴ DeepMind, London, UK.
⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
⁶ 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.
⁷ Department of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
⁸ Department of Structural and Molecular Biology, UCL, London, UK.
⁹ AlphaFold Protein Structure Database, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
¹⁰ Department of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
¹¹ Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030, USA.
¹² Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
¹³ Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
¹⁴ 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.
¹⁵ Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94157, USA. Electronic address: https://twitter.com/salilab_ucsf.
¹⁶ 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; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
¹⁷ 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.

PMID: 36828268
PMCID: PMC10293049 (available on 2024-07-15)
DOI: 10.1016/j.jmb.2023.168021

Abstract

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.

Keywords: Computed Structure Models; Data Standard; ModelCIF; PDBx/mmCIF; Protein Structure Prediction.

Publication types

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

MeSH terms

Databases, Protein*
Macromolecular Substances / chemistry
Protein Conformation
Software

Substances

Macromolecular Substances

Abstract

Publication types

MeSH terms

Substances

Grants and funding