FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

ABSTRACT: Building reliable structural models of G protein-coupled receptors (GPCRs) is a difficult task because of the paucity of suitable templates, low sequence identity, and the wide variety of ligand specificities within the superfamily. Template-based modeling is known to be the most successful method for protein structure prediction. However, refinement of homology models within 1-3 A C alpha RMSD of the native structure remains a major challenge. Here, we address this problem by developing a novel protocol (foldGPCR) for modeling the transmembrane (TM) region of GPCRs in complex with a ligand, aimed to accurately model the structural divergence between the template and target in the TM helices. The protocol is based on predicted conserved inter-residue contacts between the template and targe

SUBMITTER: Michino M 

PROVIDER: S-EPMC2933064 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature