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Int. J. Mol. Sci. 2009, 10(5), 2190-2202; doi:10.3390/ijms10052190

Identifying Protein-Protein Interaction Sites Using Covering Algorithm

* ,
The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China
* Author to whom correspondence should be addressed.
Received: 17 March 2009 / Revised: 30 April 2009 / Accepted: 13 May 2009 / Published: 15 May 2009
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Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60.86%, Trim dataset with overall accuracy) to a support vector machine and maximum entropy on our dataset, a correlation coefficient (CC) of 0.2893, 58.83% specificity, 56.12% sensitivity on the Complete dataset and 0.2144 (CC), 53.34% (specificity), 65.59% (sensitivity) on the Trim dataset in identifying interface residues by 5-fold cross-validation on 61 protein chains. This result indicates that the covering algorithm is a powerful and robust protein-protein interaction site prediction method that can guide biologists to make specific experiments on proteins. Examination of the predictions in the context of the 3-dimensional structures of proteins demonstrates the effectiveness of this method.
Keywords: protein-protein interaction; covering algorithm; sequence profile; residue accessible area; maximum entropy protein-protein interaction; covering algorithm; sequence profile; residue accessible area; maximum entropy
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Du, X.; Cheng, J.; Song, J. Identifying Protein-Protein Interaction Sites Using Covering Algorithm. Int. J. Mol. Sci. 2009, 10, 2190-2202.

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