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    Evaluating template-based and template-free protein-protein complex structure prediction

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    Authors
    Vreven, Thom
    Hwang, Howook
    Pierce, Brian G.
    Weng, Zhiping
    UMass Chan Affiliations
    Program in Bioinformatics and Integrative Biology
    Document Type
    Journal Article
    Publication Date
    2014-03-01
    Keywords
    Algorithms
    Computational Biology
    Databases, Protein
    Protein Conformation
    *Protein Interaction Domains and Motifs
    Protein Interaction Mapping
    Sequence Alignment
    Software
    Structural Homology, Protein
    Biochemistry, Biophysics, and Structural Biology
    Bioinformatics
    Computational Biology
    Integrative Biology
    Structural Biology
    Systems Biology
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    Link to Full Text
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956070/
    Abstract
    We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme-inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.
    Source
    Brief Bioinform. 2014 Mar;15(2):169-76. doi: 10.1093/bib/bbt047. Epub 2013 Jul 1. Link to article on publisher's site
    DOI
    10.1093/bib/bbt047
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/25921
    PubMed ID
    23818491
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1093/bib/bbt047
    Scopus Count
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