A simple method for predicting transmembrane alpha helices with better accuracy

The prediction of a protein's structure from its amino acid sequence has be en a long-standing goal of molecular biology. In this work, a new set of co nformational parameters for membrane spanning a helices was developed using the information from the topology of 70 membrane proteins. Based on these conformational parameters, a simple algorithm has been formulated to predic t the transmembrane a helices in membrane proteins. A FORTRAN program has b een developed which takes the amino acid sequence as input and gives the pr edicted transmembrane a-helices as output. The present method correctly ide ntifies 295 transmembrane helical segments in 70 membrane proteins with onl y two overpredictions. Furthermore, this method predicts all 45 transmembra ne helices in the photosynthetic reaction center, bacteriorhodopsin and cyt ochrome c oxidase to an 86% level of accuracy and so is better than all oth er methods published to date.