. 2023 Jul 15;435(14):168021.

doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23.

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

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
DOI: 10.1016/j.jmb.2023.168021

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

Brinda Vallat et al. J Mol Biol. 2023.

. 2023 Jul 15;435(14):168021.

doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23.

Authors

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
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.

PubMed Disclaimer

Conflict of interest statement

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.

Figures

**Figure 1.**
Schematic representation of modeling methods using target sequence(s), structure databases (*e.g*., PDB), and sequence databases (*e.g*., Uniclust30 [51]) as input to produce CSMs and estimates of prediction confidence. Homology modeling uses specific templates as its main input, while *ab initio* methods work without templates. Commonly used *ab initio* methods rely on multiple sequence alignments, which are either used directly as input for end-to-end structure prediction or processed to extract spatial restraints used to generate CSMs.

**Figure 2.**
Schematic representation of the data specifications in ModelCIF. Definitions reused from PDBx/mmCIF are shown in white boxes (*e.g*., Atomic Coordinates) and the newly added definitions are shown in gray boxes (*e.g*., Model Quality Metrics). (A) Descriptions are provided for input data used in template-based and template-free modeling. (B) Representations of molecular components are retained from PDBx/mmCIF. (C) Definitions for atomic coordinates, secondary structure features, and ensembles are taken from PDBx/mmCIF; descriptions of local and global CSM quality metrics are defined in ModelCIF. (D) Several metadata definitions from PDBx/mmCIF are reused. New metadata definitions regarding modeling protocol, CSM classification (*ab initio*, homology, *etc*.) and descriptions of associated files are included in ModelCIF. Examples of CSM-specific data and metadata represented in ModelCIF are provided in the Supplementary Material.

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources