ArticleJournal of chemical theory and computation2019
Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Non-Equilibrium Modeling of Concentration-Driven processes with Constant Chemical Potential Molecular Dynamics Simulations.Accounts of chemical research · 2023Article
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations.Annual review of food science and technology · 2020Review
- Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes.Frontiers in molecular biosciences · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations.Frontiers in molecular biosciences · 2019Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-protein-coupled receptors (GPCRs) constitute as much as 30% of the overall proteins targeted by FDA-approved drugs. However, paucity of structural experimental information and low sequence identity between members of the family impair the reliability of traditional docking approaches and atomistic molecular dynamics simulations for in silico pharmacological applications. We present here a dual-resolution approach tailored for such low-resolution models. It couples a hybrid molecular mechanics/coarse-grained (MM/CG) scheme, previously developed by us for GPCR-ligand complexes, with a Hamiltonian-based adaptive resolution scheme (H-AdResS) for the solvent. This dual-resolution approach removes potentially inaccurate atomistic details from the model while building a rigorous statistical ensemble-the grand canonical one-in the high-resolution region. We validate the method on a well-studied GPCR-ligand complex, for which the 3D structure is known, against atomistic simulations. This implementation paves the way for future accurate in silico studies of low-resolution ligand/GPCRs models.
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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.