Journal
PROTEIN SCIENCE
Volume 14, Issue 7, Pages 1723-1728Publisher
WILEY
DOI: 10.1110/ps.051395305
Keywords
topology prediction; transmembrane protein; domain assignment; prediction constraints
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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.
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