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    Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

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    Authors
    Lensink, Marc F.
    Weng, Zhiping
    Vreven, Thom
    Pierce, Brian G.
    Borrman, Tyler M.
    UMass Chan Affiliations
    Program in Bioinformatics and Integrative Biology
    Document Type
    Journal Article
    Publication Date
    2016-04-28
    Keywords
    CAPRI
    CASP
    oligomer state
    blind prediction
    protein interaction
    protein docking
    Bioinformatics
    Computational Biology
    Genomics
    Structural Biology
    
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    Link to Full Text
    http://dx.doi.org/10.1002/prot.25007
    Abstract
    We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.
    Source
    Proteins. 2016 Apr 28. doi: 10.1002/prot.25007. Link to article on publisher's site
    DOI
    10.1002/prot.25007
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/25945
    PubMed ID
    27122118
    Notes

    Full author list omitted for brevity. For full list see article.

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    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1002/prot.25007
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