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TMBETADISC-RBF: Discrimination of -barrel membrane proteins using RBF networks and PSSM profiles by Yu-Yen Ou; M.Michael Gromiha; Shu-An Chen; Makiko Suwa is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important task both for identifying OMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. We have developed a method based on radial basis function networks and position specific scoring matrix (PSSM) profiles generated by PSI-BLAST and nonredundant protein database. Our approach with PSSM profiles has correctly predicted the OMPs with a cross-validated accuracy of 96.4% in a set of 1251 proteins, which contain 206 OMPs, 667 globular proteins and 378 ␣-helical inner membrane proteins. Furthermore, we applied our method on a dataset containing 114 OMPs, 187 TMH proteins and 195 globular proteins obtained with less than 20% sequence identity and obtained the cross-validated accuracy of 95%. This accuracy of discriminating OMPs is higher than other methods in the literature and our method could be used as an effective tool for dissecting OMPs from genomic sequences. We have developed a prediction server, TMBETADISC-RBF, which is available at http://rbf.bioinfo.tw/ sachen/OMP.html.

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Author

Yu-Yen Ou; M.Michael Gromiha; Shu-An Chen; Makiko Suwa

Publisher

Elsevier Science; Elsevier ; Elsevier Ltd.; Elsevier BV (ISSN 1476-9271)

Published

2008

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)