A simple method for predicting transmembrane {alpha} helices with better accuracy

The prediction of a protein's structure from its amino acidsequence has been a long-standing goal of molecular biology.In this work, a new set of conformational parameters for membranespanning helices was developed using the information from thetopology of 70 membrane proteins. Based on these conformationalparameters, a simple algorithm has been formulated to predictthe transmembrane helices in membrane proteins. A FORTRAN programhas been developed which takes the amino acid sequence as inputand gives the predicted transmembrane -helices as output. Thepresent method correctly identifies 295 transmembrane helicalsegments in 70 membrane proteins with only two overpredictions.Furthermore, this method predicts all 45 transmembrane helicesin the photosynthetic reaction center, bacteriorhodopsin andcytochrome c oxidase to an 86% level of accuracy and so is betterthan all other methods published to date.