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- Title
patGPCR: A Multitemplate Approach for Improving 3D Structure Prediction of Transmembrane Helices of G-Protein-Coupled Receptors.
- Authors
Hongjie Wu; Qiang Lü; Lijun Quan; Peide Qian; Xiaoyan Xia
- Abstract
The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a "super" template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TMRMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multipletemplate MODELLER.
- Subjects
G protein coupled receptors; PREDICTION models; MEMBRANE proteins; HOMOLOGY (Biochemistry); PROTEIN structure; MOLECULAR docking
- Publication
Computational & Mathematical Methods in Medicine, 2013, p1
- ISSN
1748-670X
- Publication type
Article
- DOI
10.1155/2013/486125