Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier.

Haijiang Geng,Fangrong Yan,Xiao Lin,Yu Liu,Tao Lu

doi:10.1155/2015/978193

Abstract

Protein functions through interactions with other proteins and biomolecules and these interactions occur on the so-called interface residues of the protein sequences. Identifying interface residues makes us better understand the biological mechanism of protein interaction. Meanwhile, information about the interface residues contributes to the understanding of metabolic, signal transduction networks and indicates directions in drug designing. In recent years, researchers have focused on developing new computational methods for predicting protein interface residues. Here we creatively used a 181-dimension protein sequence feature vector as input to the Naive Bayes Classifier- (NBC-) based method to predict interaction sites in protein-protein complexes interaction. The prediction of interaction sites in protein interactions is regarded as an amino acid residue binary classification problem by applying NBC with protein sequence features. Independent test results suggested that Naive Bayes Classifier-based method with the protein sequence features as input vectors performed well.

Highlights

A protein exerts its biological functions through interactions with other biomacromolecules, and these interactions occur on the residues of protein amino acid sequences
To investigate the distribution of the known interface residues in protein sequences of the training and testing dataset, we calculated the number of neighboring interface residues for each position aside from the target residue from N-terminal side of an interface residue to C-terminal side and the results are shown in Figures 2 and 3
These results clearly indicate that interface residues have a tendency of clustering in protein sequences

Summary

Introduction

A protein exerts its biological functions through interactions with other biomacromolecules, and these interactions occur on the residues of protein amino acid sequences. All the potential interaction sites, which the protein biochemical interactions occurred on, are on the surface of protein 3D conformation and called interface residues. Knowing the specific interface residues of proteins contributes to better understanding of protein-protein interaction mechanism. It is significant for researchers to be aware of interfaces residues in the study of protein mimetic engineering, molecular pathways elucidation, drug designing, and so on [1,2,3]. There is a desperate need to develop new convenient and accurate computational ways of identifying protein-protein interface residues [4]. Discovered approach is utilizing all kinds of protein sequence and amino acid residue feature information to predict protein interfaces residues by using statistical classification methods

Methods

Results

Conclusion