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Improved membrane protein topology prediction by domain assignments
Author(s) -
Bernsel Andreas,
Von Heijne Gunnar
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.051395305
Subject(s) - topology (electrical circuits) , membrane topology , membrane protein , integral membrane protein , ferm domain , computational biology , protein domain , membrane , genome , biology , computer science , biological system , gene , biochemistry , mathematics , combinatorics
Topology predictions for integral membrane proteins can be substantially improved if parts of the protein can be constrained to a given in/out location relative to the membrane using experimental data or other information. Here, we have identified a set of 367 domains in the SMART database that, when found in soluble proteins, have compartment‐specific localization of a kind relevant for membrane protein topology prediction. Using these domains as prediction constraints, we are able to provide high‐quality topology models for 11% of the membrane proteins extracted from 38 eukaryotic genomes. Two‐thirds of these proteins are single spanning, a group of proteins for which current topology prediction methods perform particularly poorly.