Support Vector Machine for predicting α-turn types

Tight turns play an important role in globular proteins from both the structural and functional points of view. Of tight turns, P-turns and gamma-turns have been extensively studied, but alpha-turns were little investigated. Recently, a systematic search for alpha-turns classified alpha-turns into nine different types according to their backbone trajectory features. In this paper, Support Vector Machines (SVMs), a new machine learning method, is proposed for predicting the alpha-turn types in proteins. The high rates of correct prediction imply that that the formation of different alpha-turn types is evidently correlated with the sequence of a pentapeptide, and hence can be approximately predicted based on the sequence information of the pentapeptide alone, although the incorporation of its interaction with the other part of a protein, the so-called long distance interaction, will further improve the prediction quality. (C) 2003 Elsevier Science Inc. All rights reserved.