title: 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 alpha-helix and beta-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 beta-turns and most of the rest are gamma-turns. Analysis and prediction of beta-turns and gamma-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 beta-turns and gamma-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict beta-turns and gamma-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 beta-turns and gamma-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.
authors.affiliation: Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan. h-pham@jaist.ac.jp
authors.forename: Tho Hoan
authors.initials: TH
authors.lastname: Pham
authors.forename: Kenji
authors.initials: K
authors.lastname: Satou
authors.forename: Tu Bao
authors.initials: TB
authors.lastname: Ho
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D001185:Artificial Intelligence; D016000:Cluster Analysis; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D000596:Amino Acids; D011506:Proteins