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    Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

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    Authors
    Lensink, Marc F.
    Vreven, Thom
    Vangaveti, Sweta
    Borrman, Tyler M.
    Weng, Zhiping
    Wodak, Shoshana J.
    UMass Chan Affiliations
    Program in Bioinformatics and Integrative Biology
    Document Type
    Journal Article
    Publication Date
    2019-12-01
    Keywords
    CAPRI
    CASP
    blind prediction
    docking
    oligomeric state
    protein assemblies
    protein complexes
    protein-protein interaction
    template-based modeling
    Amino Acids, Peptides, and Proteins
    Biochemistry, Biophysics, and Structural Biology
    Bioinformatics
    Computational Biology
    Integrative Biology
    Systems Biology
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    Link to Full Text
    https://doi.org/10.1002/prot.25838
    Abstract
    We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
    Source

    Proteins. 2019 Dec;87(12):1200-1221. doi: 10.1002/prot.25838. Epub 2019 Oct 25. Link to article on publisher's site

    DOI
    10.1002/prot.25838
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/25868
    PubMed ID
    31612567
    Notes

    Full author list omitted for brevity. For the full list of authors, see article.

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    ae974a485f413a2113503eed53cd6c53
    10.1002/prot.25838
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