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    Performance of ZDOCK in CAPRI rounds 20-26

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    Authors
    Vreven, Thom
    Pierce, Brian G.
    Hwang, Howook
    Weng, Zhiping
    UMass Chan Affiliations
    Program in Bioinformatics and Integrative Biology
    Document Type
    Journal Article
    Publication Date
    2013-10-03
    Keywords
    Protein-protein docking. Protein-protein interaction
    Complexes
    ZRANK
    IRAD
    Bioinformatics
    Computational Biology
    
    Metadata
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    Link to Full Text
    http://dx.doi.org/10.1002/prot.24432
    Abstract
    We report the performance of our approaches for protein-protein docking and interface analysis in CAPRI rounds 20-26. At the core of our pipeline was the ZDOCK program for rigid-body protein-protein docking. We then reranked the ZDOCK predictions using the ZRANK or IRAD scoring functions, pruned and analyzed energy landscapes using clustering, and analyzed the docking results using our interface prediction approach RCF. When possible, we used biological information from the literature to apply constraints to the search space during or after the ZDOCK runs. For approximately half of the standard docking challenges we made at least one prediction that was acceptable or better. For the scoring challenges we made acceptable or better predictions for all but one target. This indicates that our scoring functions are generally able to select the correct binding mode. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.
    Source
    Proteins. 2013 Oct 3. doi: 10.1002/prot.24432. Link to article on publisher's site
    DOI
    10.1002/prot.24432
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/30025
    PubMed ID
    24123140
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1002/prot.24432
    Scopus Count
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    UMass Chan Faculty and Researcher Publications
    Program in Bioinformatics and Integrative Biology Publications

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