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
Date Published2014 Mar

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.

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