Prediction of membrane spanning segments and topology in beta-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, TMBETAPRED-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.
Ou
Yu-Yen
YY
Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan.
Chen
Shu-An
SA
Gromiha
M Michael
MM
D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D017433:Protein Structure, Secondary
D001425:Bacterial Outer Membrane Proteins