Journal
BRIEFINGS IN BIOINFORMATICS
Volume 15, Issue 2, Pages 169-176Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbt047
Keywords
protein-protein structure; template-based prediction; protein-protein docking; ZDOCK; PRISM; COTH
Funding
- National Institutes of Health [R01 GM084884]
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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.
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