ArticleNucleic acids research2016
GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- Ligand and Residue Free Energy Perturbations Solve the Dual Binding Mode Proposal for an AThe journal of physical chemistry. B · 2025Article
- Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies.Molecules (Basel, Switzerland) · 2024Review
- Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell.Bioinformatics (Oxford, England) · 2024Article
- Opsin expression varies across larval development and taxa in pteriomorphian bivalves.Frontiers in neuroscience · 2024Article
- Homology Modeling of the G Protein-Coupled Receptors.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cancer-Related Somatic Mutations in Transmembrane Helices Alter Adenosine A1 Receptor Pharmacology.Molecules (Basel, Switzerland) · 2022Article
- AJournal for immunotherapy of cancer · 2022Article
- Slow conformational dynamics of the human AStructure (London, England : 1993) · 2022Article
- Exploring Non-orthosteric Interactions with a Series of Potent and Selective AACS medicinal chemistry letters · 2022Article
- Review
- GPCRsignal: webserver for analysis of the interface between G-protein-coupled receptors and their effector proteins by dynamics and mutations.Nucleic acids research · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Activation of GPR37 in macrophages confers protection against infection-induced sepsis and pain-like behaviour in mice.Nature communications · 2021Article
- Free Energy Calculations for Protein-Ligand Binding Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Review
- BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling.Frontiers in molecular biosciences · 2021Article
- G-Protein coupled receptors: structure and function in drug discovery.RSC advances · 2020Review
- Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor HJournal of computer-aided molecular design · 2020Article
- Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs.PLoS computational biology · 2020Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.
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