Prediction of protein secondary structure content

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.