Prediction of protein-protein interaction sites using support vector machines
نویسندگان
چکیده
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. 3 INTRODUCTION Proteins perform a biological function by interacting with other proteins, compounds, RNA,
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Prediction of Protein Interaction Sites and Protein-Protein Interaction Pairs Using Support Vector Machines
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