ArticleInternational journal of molecular sciences2019
A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
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- Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis.International journal of molecular sciences · 2024Article
- Allosteric Modulators of Dopamine DMolecules (Basel, Switzerland) · 2022Review
- Funnel metadynamics and behavioral studies reveal complex effect of D2AAK1 ligand on anxiety-like processes.Scientific reports · 2022Article
- Effect of Ions and Sequence Variants on the Antagonist Binding Properties of the Histamine HInternational journal of molecular sciences · 2022Article
- Dynamic recognition of naloxone, morphine and endomorphin1 in the same pocket of µ-opioid receptors.Frontiers in molecular biosciences · 2022Article
- Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs.Advances in protein chemistry and structural biology · 2022Review
- Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands.Frontiers in endocrinology · 2022Review
- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Molecular Modeling of Histamine Receptors-Recent Advances in Drug Discovery.Molecules (Basel, Switzerland) · 2021Review
- Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm.BMC bioinformatics · 2021Article
- Agonist Binding and G Protein Coupling in Histamine HInternational journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
G protein-coupled receptors (GPCRs) are a main drug target and therefore a hot topic in pharmaceutical research. One important prerequisite to understand how a certain ligand affects a GPCR is precise knowledge about its binding mode and the specific underlying interactions. If no crystal structure of the respective complex is available, computational methods can be used to deduce the binding site. One of them are metadynamics simulations which have the advantage of an enhanced sampling compared to conventional molecular dynamics simulations. However, the enhanced sampling of higher-energy states hampers identification of the preferred binding mode. Here, we present a novel protocol based on clustering of multiple walker metadynamics simulations which allows identifying the preferential binding mode from such conformational ensembles. We tested this strategy for three different model systems namely the histamine H
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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.