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

Databases, Protein Macromolecular Substances / chemistry Protein Conformation Software
Computed Structure Models Data Standard ModelCIF PDBx/mmCIF Protein Structure Prediction

Journal

Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R

Informations de publication

Date de publication:
15 07 2023
Historique:
received: 29 11 2022
revised: 15 02 2023
accepted: 16 02 2023
pmc-release: 15 07 2024
medline: 27 6 2023
pubmed: 25 2 2023
entrez: 24 2 2023
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.jmb.2023.168021 PMID: 36828268 PMC: PMC10293049
pubmed: 36828268
pii: S0022-2836(23)00077-3
doi: 10.1016/j.jmb.2023.168021
pmc: PMC10293049
mid: NIHMS1877877
pii:
doi:

Substances chimiques

Macromolecular Substances 0

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

168021

Subventions

Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S020071/1
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : R01 GM083960
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM109046
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM133198
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/W017970/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S020144/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/V004247/1
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : U01 GM093324
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM109824
Pays : United States

Informations de copyright

Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Auteurs

Brinda Vallat (B)

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.

Gerardo Tauriello (G)

Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Stefan Bienert (S)

Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Juergen Haas (J)

Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Benjamin M Webb (BM)

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.

Augustin Žídek (A)

DeepMind, London, UK.

Wei Zheng (W)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Ezra Peisach (E)

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.

Dennis W Piehl (DW)

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.

Ivan Anischanka (I)

Department of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.

Ian Sillitoe (I)

Department of Structural and Molecular Biology, UCL, London, UK.

James Tolchard (J)

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.

Mihaly Varadi (M)

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.

David Baker (D)

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.

Christine Orengo (C)

Department of Structural and Molecular Biology, UCL, London, UK.

Yang Zhang (Y)

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Jeffrey C Hoch (JC)

Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030, USA.

Genji Kurisu (G)

Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

Ardan Patwardhan (A)

Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.

Sameer Velankar (S)

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.

Stephen K Burley (SK)

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.

Andrej Sali (A)

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.

Torsten Schwede (T)

Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Helen M Berman (HM)

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.

John D Westbrook (JD)

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.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Bases de données de protéines › ModelCIF: An Extension of PDBx/mmCIF Data...
questionsmedicales.fr › Structures macromoléculaires › ModelCIF: An Extension of PDBx/mmCIF Data...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › ModelCIF: An Extension of PDBx/mmCIF Data...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › ModelCIF: An Extension of PDBx/mmCIF Data...