SUPPORT VECTOR MACHINES FOR PREDICTION AND ANALYSIS OF BETA AND GAMMA-TURNS IN PROTEINS
Abstract
Tight turns have long been recognized as one of the three important features of proteins, together with α-helix and β-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are β-turns and most of the rest are γ-turns. Analysis and prediction of β-turns and γ-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of β-turns and γ-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict β-turns and γ-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of β-turns and γ-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.
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