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

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TitleEvaluating template-based and template-free protein-protein complex structure prediction.
Publication TypeJournal Article
Year of Publication2014
AuthorsVreven, T, Hwang, H, Pierce, BG, Weng, Z
JournalBrief Bioinform
Volume15
Issue2
Pagination169-76
Date Published2014 Mar
ISSN1477-4054
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.

DOI10.1093/bib/bbt047
Alternate JournalBrief. Bioinformatics
PubMed ID23818491
PubMed Central IDPMC3956070
Grant ListR01 GM084884 / GM / NIGMS NIH HHS / United States