Publication
Title
Improved detection of homologous membrane proteins by inclusion of information from topology predictions
Author
Abstract
A total of 20%-25% of the proteins in a typical genome are helical membrane proteins. The transmembrane regions of these proteins have markedly different properties when compared with globular proteins. This presents a problem when homology search algorithms optimized for globular proteins are applied to membrane proteins. Here we present modifications of the standard Smith-Waterman and profile search algorithms that significantly improve the detection of related membrane proteins. The improvement is based on the inclusion of information about predicted transmembrane segments in the alignment algorithm. This is done by simply increasing the alignment score if two residues predicted to belong to transmembrane segments are aligned with each other. Benchmarking over a test set of G-protein-coupled receptor sequences shows that the number of false positives is significantly reduced in this way, both when closely related and distantly related proteins are searched for.
Language
English
Source (journal)
Protein science. - Cambridge
Publication
Cambridge : 2002
ISSN
0961-8368
Volume/pages
11:3(2002), p. 652-658
ISI
000173931900020
Full text (Publishers DOI)
Full text (publishers version - intranet only)
UAntwerpen
Faculty/Department
Publication type
Subject
External links
Web of Science
Record
Identification
Creation 11.03.2013
Last edited 20.04.2017