ArticlePLoS computational biology2014
High-resolution modeling of transmembrane helical protein structures from distant homologues.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 36 citations in OpenAlex.
- Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks.Nature chemistry · 2025Article
- Computationally designed GPCR quaternary structures bias signaling pathway activation.Nature communications · 2022Article
- Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction.AMB Express · 2022Article
- Computational design of G Protein-Coupled Receptor allosteric signal transductions.Nature chemical biology · 2020Article
- A benchmark study of loop modeling methods applied to G protein-coupled receptors.Journal of computer-aided molecular design · 2019Article
- PiPred - a deep-learning method for prediction of π-helices in protein sequences.Scientific reports · 2019Article
- Molecular Modeling of Drug-Transporter Interactions-An International Transporter Consortium Perspective.Clinical pharmacology and therapeutics · 2018Review
- Reprogramming G protein coupled receptor structure and function.Current opinion in structural biology · 2018Review
- Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.Structure (London, England : 1993) · 2017Article
- Computational design of ligand-binding membrane receptors with high selectivity.Nature chemical biology · 2017Article
- Toward high-resolution computational design of the structure and function of helical membrane proteins.Nature structural & molecular biology · 2016Article
- An Integrated Framework Advancing Membrane Protein Modeling and Design.PLoS computational biology · 2015Article
- Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy.Nature communications · 2015Article
- Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.Journal of computer-aided molecular design · 2015Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Eukaryotic transmembrane helical (TMH) proteins perform a wide diversity of critical cellular functions, but remain structurally largely uncharacterized and their high-resolution structure prediction is currently hindered by the lack of close structural homologues. To address this problem, we present a novel and generic method for accurately modeling large TMH protein structures from distant homologues exhibiting distinct loop and TMH conformations. Models of the adenosine A2AR and chemokine CXCR4 receptors were first ranked in GPCR-DOCK blind prediction contests in the receptor structure accuracy category. In a benchmark of 50 TMH protein homolog pairs of diverse topology (from 5 to 12 TMHs), size (from 183 to 420 residues) and sequence identity (from 15% to 70%), the method improves most starting templates, and achieves near-atomic accuracy prediction of membrane-embedded regions. Unlike starting templates, the models are of suitable quality for computer-based protein engineering: redesigned models and redesigned X-ray structures exhibit very similar native interactions. The method should prove useful for the atom-level modeling and design of a large fraction of structurally uncharacterized TMH proteins from a wide range of structural homologues.
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