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TMBETADISC-RBF: Discrimination of β-barrel membrane proteins using RBF networks and PSSM profiles

Paper ID Volume ID Publish Year Pages File Format Full-Text
15335 1404 2008 5 PDF Available
Title
TMBETADISC-RBF: Discrimination of β-barrel membrane proteins using RBF networks and PSSM profiles
Abstract

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 non-redundant 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 α-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.

Keywords
Outer membrane protein; Discrimination; Radial basis function; PSSM profile
First Page Preview
TMBETADISC-RBF: Discrimination of β-barrel membrane proteins using RBF networks and PSSM profiles
Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 3, June 2008, Pages 227–231
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering