Identifying protein-protein interaction sites using covering algorithm.
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.
Du
Xiuquan
X
The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China.
Cheng
Jiaxing
J
The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China.
Song
Jie
J
The Key Laboratory of Intelligent Computing and Signal Processing, Ministry of Education, Anhui University, Anhui, China.
D000465:Algorithms; D000595:Amino Acid Sequence; D019277:Entropy; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D060388:Support Vector Machine
D011506:Proteins