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J Theor Biol. 2012 Jan 21;293:143-50. doi: 10.1016/j.jtbi.2011.10.021. Epub 2011 Oct 25.

Prediction of protein-protein interaction sites using patch-based residue characterization.

Author information

1
The State Key Laboratory of Structural Analysis of Industrial Equipment, Dalian University of Technology, 2 Ling-Gong Road, Dalian 116024, China.

Abstract

Identifying protein-protein interaction sites provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Using a patch-based model for residue characterization, we trained random forest classifiers for residue-based interface prediction, which was followed by a clustering procedure to produce patches for patch-based interface prediction. For residue-based interface prediction, our method achieves a specificity rate of 0.7 and a sensitivity rate of 0.78. For patch-based interface prediction, a success rate of 0.80 is achieved. Based on same datasets, we also compare it with several published methods. The results show that our method is a successful predictor for residue-based and patch-based interface prediction.

PMID:
22037062
DOI:
10.1016/j.jtbi.2011.10.021
[Indexed for MEDLINE]

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