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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
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Received: 17 March 2009 / Revised: 30 April 2009 / Accepted: 13 May 2009 / Published: 15 May 2009
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Abstract

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
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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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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