ArticleBiochimica et biophysica acta. General subjects2020
Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor.
Article in Biochimica et biophysica acta. General subjects, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Molecular Dynamics and Other HPC Simulations for Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (International journal of molecular sciences · 2023Article
- In Silico Design of a Chimeric Humanized L-asparaginase.International journal of molecular sciences · 2023Article
- Molecular Simulations and Drug Discovery of Adenosine Receptors.Molecules (Basel, Switzerland) · 2022Review
- Screening and identification of phytochemical drug molecules against mutant BRCA1 receptor of breast cancer using computational approaches.Molecular and cellular biochemistry · 2022Article
- Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery.Frontiers in molecular biosciences · 2022Article
- From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.Frontiers in pharmacology · 2022Review
- Gaussian accelerated molecular dynamics (GaMD): principles and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundEnsemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A
methodsEnsemble docking that integrates Gaussian accelerated molecular dynamic (GaMD) simulations and molecular docking using Autodock has been implemented for retrospective docking of known positive allosteric modulators (PAMs) in the A
resultsEnsemble docking outperforms docking of the receptor cryo-EM structure. The calculated docking enrichment factors (EFs) and the area under the receiver operating characteristic curves (AUC) are significantly increased.
conclusionsReceptor ensembles generated from GaMD simulations are able to increase the success rate of discovering PAMs of A GENERAL SIGNIFICANCE: Ensemble docking is a promising approach for drug discovery targeting flexible receptors.
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Registered trials
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