Title
Improved detection of homologous membrane proteins by inclusion of information from topology predictions Improved detection of homologous membrane proteins by inclusion of information from topology predictions
Author
Faculty/Department
Faculty of Pharmaceutical, Biomedical and Veterinary Sciences. Pharmacy
Publication type
article
Publication
Cambridge ,
Subject
Chemistry
Biology
Source (journal)
Protein science. - Cambridge
Volume/pages
11(2002) :3 , p. 652-658
ISSN
0961-8368
ISI
000173931900020
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
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.
E-info
https://repository.uantwerpen.be/docman/iruaauth/f1d697/d4f2962.pdf
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