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Improved membrane protein topology prediction by domain assignments

Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
Stockholm Bioinformatics Center, AlbaNova, SE-106 91 Stockholm, Sweden

(RECEIVED February 3, 2005; FINAL REVISION April 17, 2005; ACCEPTED April 17, 2005)

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.

Keywords: topology prediction; transmembrane protein; domain assignment; prediction constraints

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051395305.

Reprint requests to: Gunnar von Heijne, Stockholm University, SE- 106 91 Stockholm, Sweden; e-mail: gunnar{at}dbb.su.se; fax: +46-8-15- 36-79.

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