Prediction of membrane spanning segments and topology in β‐barrel membrane proteins at better accuracy

Prediction of membrane spanning segments in β‐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 β‐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 β‐strand segments. The β‐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, TMBETAPRED‐RBF for predicting the transmembrane β‐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 β‐barrel membrane proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010