ArticleProteins2010
FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.Journal of chemical theory and computation · 2017Article
- OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
- Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.Journal of computational chemistry · 2016Article
- GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors.BMC bioinformatics · 2015Article
- Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.Journal of computer-aided molecular design · 2015Article
- Computational modeling of membrane proteins.Proteins · 2015Review
- Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.BMC biophysics · 2014Article
- Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop.Biophysical journal · 2013Article
- Membrane protein native state discrimination by implicit membrane models.Journal of computational chemistry · 2013Article
- Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.Journal of computer-aided molecular design · 2013Article
- Article
- patGPCR: a multitemplate approach for improving 3D structure prediction of transmembrane helices of G-protein-coupled receptors.Computational and mathematical methods in medicine · 2013Article
- Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations.Proteins · 2012Article
- Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site.Journal of biomedicine & biotechnology · 2012Article
- From laptop to benchtop to bedside: structure-based drug design on protein targets.Current pharmaceutical design · 2012Review
- Enhanced Inter-helical Residue Contact Prediction in Transmembrane Proteins.Chemical engineering science · 2011Article
- GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.BMC bioinformatics · 2011Article
- Predicting structurally conserved contacts for homologous proteins using sequence conservation filters.Proteins · 2009Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
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 target, and exploits an all-atom implicit membrane force field. The placement of the ligand in the binding pocket is guided by biochemical data. The foldGPCR protocol is implemented by a stepwise hierarchical approach, in which the TM helical bundle and the ligand are assembled by simulated annealing trials in the first step, and the receptor-ligand complex is refined with replica exchange sampling in the second step. The protocol is applied to model the human beta(2)-adrenergic receptor (beta(2)AR) bound to carazolol, using contacts derived from the template structure of bovine rhodopsin. Comparison with the X-ray crystal structure of the beta(2)AR shows that our protocol is particularly successful in accurately capturing helix backbone irregularities and helix-helix packing interactions that distinguish rhodopsin from beta(2)AR.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.