Prediction of Membrane Spanning Segments and Topology in β-Barrel Membrane Proteins at Better Accuracy

Prediction of membrane spanning segments in beta-barrel outer membrane proteins (OMP) and their topology is an important problem in structural and functional genomics. In this work, we propose a method based on radial basis networks for predicting the number of beta-strands in OMPs and identifying their membrane spanning segments. Our method showed a leave-one-out cross validation accuracy of 96% in a set of 28 OMPs, which have the range of 8-22 beta-strand segments. The beta-strand segments in OMPs and the residues in membrane spanning segments are correctly predicted with the accuracy of 96% and 87%, respectively. We have developed a web server, TMBE-TAPRED-RBF for predicting the transmembrane beta-strands from amino acid sequence and it is available at http:// rbf.bioinfo.tw/sachen/tmrbf.html. We Suggest that our method could be an effective tool for predicting the membrane spanning regions and topology of beta-barrel membrane proteins. (c) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 217-223, 2010