Evidence map›Paper›PMID 36828268›Full record

ArticleJournal of molecular biology2023

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 and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Brinda VallatResearch 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 TaurielloBiozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Stefan BienertBiozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Juergen HaasBiozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Benjamin M WebbDepartment 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 ŽídekDeepMind, London, UK.
Wei ZhengDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Ezra PeisachResearch 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 PiehlResearch 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 AnischankaDepartment of Biochemistry, and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Ian SillitoeDepartment of Structural and Molecular Biology, UCL, London, UK.
James TolchardAlphaFold 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 VaradiAlphaFold 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 BakerDepartment 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 OrengoDepartment of Structural and Molecular Biology, UCL, London, UK.
Yang ZhangDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Jeffrey C HochBiological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030, USA.
Genji KurisuProtein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Ardan PatwardhanElectron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Sameer VelankarAlphaFold 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 BurleyResearch 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 SaliDepartment 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 SchwedeBiozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
Helen M BermanResearch 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 WestbrookResearch 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.

Funding

PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSR01GM133198 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BURLEY, STEPHEN K · 2019 to 2023
$19.3M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
The Protein Structure Inittiative KnowledgebaseU01GM093324 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BERMAN, HELEN M · 2010 to 2015
$12.9M
The BMRB as an evolving resource for biomolecular structure-function researchR01GM109046 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI HOCH, JEFFREY C · 2014 to 2022
$6.6M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Biotechnology and Biological Sciences Research Council BB/S020071/1Biotechnology and Biological Sciences Research Council BB/S020144/1Biotechnology and Biological Sciences Research Council BB/V004247/1Biotechnology and Biological Sciences Research Council BB/W017970/1Howard Hughes Medical InstituteNIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM109046NIGMS NIH HHS R01 GM133198NIGMS NIH HHS U01 GM093324
6 · The paper itself

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.

Indexed as

Databases, ProteinMacromolecular SubstancesProtein ConformationSoftwareMacromolecular SubstancesComputed Structure ModelsData StandardModelCIFPDBx/mmCIFProtein Structure Prediction

Identifiers

PMID36828268
PMCPMC10293049

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.