title: Prediction of protein secondary structure content.
abstract: All existing algorithms for predicting the content of protein secondary structure elements have been based on the conventional amino-acid-composition, where no sequence coupling effects are taken into account. In this article, an algorithm was developed for predicting the content of protein secondary structure elements that was based on a new amino-acid-composition, in which the sequence coupling effects are explicitly included through a series of conditional probability elements. The prediction was examined by a self-consistency test and an independent dataset test. Both indicated a remarkable improvement obtained when using the current algorithm to predict the contents of alpha-helix, beta-sheet, beta-bridge, 3(10)-helix, pi-helix, H-bonded turn, bend and random coil. Examples of the improved accuracy by introducing the new amino-acid-composition, as well as its impact on the study of protein structural class and biologically function, are discussed.
authors.affiliation: Computer-Aided Drug Discovery, Pharmacia and Upjohn, Kalamazoo, MI 49007-4940, USA.
authors.forename: W
authors.initials: W
authors.lastname: Liu
authors.forename: K C
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D016208:Databases, Factual; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011336:Probability; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids