Identifying Protein-Protein Interaction Sites Using Covering Algorithm

International Journal of Molecular Sciences

Xiuquan Du¹  Jiaxing Cheng² 

[1] The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China

关键词: protein-protein interaction;    covering algorithm;    sequence profile;    residue accessible area;    maximum entropy;   

DOI  :  10.3390/ijms10052190

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.