Paper Info
Title
Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach.
Abstract
In this paper, we describe a machine learning approach for sequence-based prediction of protein-protein interaction sites. A support vector machine (SVM) classifier was trained to predict whether or not a surface residue is an interface residue (i.e., is located in the protein-protein interaction surface), based on the identity of the target residue and its ten sequence neighbors. Separate classifiers were trained on proteins from two categories of complexes, antibody-antigen and protease-inhibitor. The effectiveness of each classifier was evaluated using leave-one-out (jack-knife) cross-validation. Interface and non-interface residues were classified with relatively high sensitivity (82.3% and 78.5%) and specificity (81.0% and 77.6%) for proteins in the antigen-antibody and protease-inhibitor complexes, respectively. The correlation between predicted and actual labels was 0.430 and 0.462, indicating that the method performs substantially better than chance (zero correlation). Combined with recently developed methods for identification of surface residues from sequence information, this offers a promising approach to predict residues involved in protein-protein interactions from sequence information alone.
Year
DOI
Venue
2004
10.1007/s00521-004-0414-3
Neural Computing and Applications
Keywords
DocType
Volume
protein-protein interaction site,antigen-antibody complex,target residue,sequence information,non-interface residue,protein-protein interaction,promising approach,support vector machine approach,surface residue,sequence neighbor,protein-protein interaction surface,interface residue
Journal
13
Issue
ISSN
Citations 
2
0941-0643
11
PageRank 
References 
Authors
2.11
4
3
Name
Order
Citations
PageRank
Changhui Yan119617.58
Vasant Honavar23353468.10
Drena Dobbs342335.43