PEDS Advance Access originally published online on January 20, 2004
Protein Engineering Design and Selection 2004 17(2):165-173; doi:10.1093/protein/gzh020
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© 2004 Oxford University Press
Prediction of protein–protein interaction sites using support vector machines
1Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, Kiban-3A1 (CB01), 1-5-1 Kashiwanoha Kashiwa, Chiba, 277-8561 and 2Central Research Laboratory, Hitachi Ltd, 1-280 Higashi-koigakubo Kokubunji City, Tokyo, 185-8601, Japan
3 To whom correspondence should be addressed at the first address. e-mail:akoike{at}hgc.jp
The identification of protein–protein interaction sites is essential for the mutant design and prediction of protein–protein networks. The interaction sites of residue units were predicted using support vector machines (SVM) and the profiles of sequentially/spatially neighboring residues, plus additional information. When only sequence information was used, prediction performance was highest using the feature vectors, sequentially neighboring profiles and predicted interaction site ratios, which were calculated by SVM regression using amino acid compositions. When structural information was also used, prediction performance was highest using the feature vectors, spatially neighboring residue profiles, accessible surface areas, and the with/without protein interaction sites ratios predicted by SVM regression and amino acid compositions. In the latter case, the precision at recall = 50% was 54–56% for a homo–hetero mixed test set and >20% higher than for random prediction. Approximately 30% of the residues wrongly predicted as interaction sites were the closest sequentially/spatially neighboring on the interaction site residues. The predicted residues covered 86–87% of the actual interfaces (96–97% of interfaces with over 20 residues). This prediction performance appeared to be slightly higher than a previously reported study. Comparing the prediction accuracy of each molecule, it seems to be easier to predict interaction sites for stable complexes.
Received October 10, 2003; revised December 25, 2003; accepted December 31, 2003 Edited by Gideon Schreiber
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