PEDS Advance Access published online on January 20, 2004
Protein Engineering Design and Selection, doi:10.1093/protein/gzh020
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1 Dept. of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, Kiban-3A1(CB01) 1-5-1 Kashiwanoha Kashiwa, Chiba, 277-8561, Japan; Central Research Laboratory, Hitachi Ltd. 1-280 Higashi-koigakubo Kokubunji city, Tokyo, 185-8601, Japan
* To whom correspondence should be addressed. 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 more than 20% higher than for random prediction. About 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 previously reported study. Comparing prediction accuracy of each molecule, it seems to be easier to predict interaction sites for stable complexes.
Keywords:
protein interaction site, support vector machine, interaction site ratio, accessible surface area, hydrophobicity
Revised December 25, 2003
Accepted December 31, 2003
Oxford University Press
Article
Prediction of protein-protein interaction sites using support vector machines
2 Dept. of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, Kiban-3A1(CB01) 1-5-1 Kashiwanoha Kashiwa, Chiba, 277-8561, Japan
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