Evaluating template-based and template-free protein-protein complex structure prediction
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDocument Type
Journal ArticlePublication Date
2014-03-01Keywords
AlgorithmsComputational 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
Metadata
Show full item recordAbstract
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 siteDOI
10.1093/bib/bbt047Permanent Link to this Item
http://hdl.handle.net/20.500.14038/25921PubMed ID
23818491Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1093/bib/bbt047
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