ArticleMethods in molecular biology (Clifton, N.J.)2024
Accelerating Molecular Dynamics Simulations for Drug Discovery.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Design, synthesis and biological evaluation of N-phenylphthalimide derivatives as potential protoporphyrinogen IX oxidase inhibitors.Pest management science · 2026Article
- Mechanisms of Peptide Agonist Dissociation and Deactivation of Adhesion G-Protein-Coupled Receptors.Biochemistry · 2025Article
- Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors.bioRxiv : the preprint server for biology · 2024Article
- AlphaFold2 in biomedical research: facilitating the development of diagnostic strategies for disease.Frontiers in molecular biosciences · 2024Review
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Authors and funding
6 authors.
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Abstract
Accurate prediction of ligand binding thermodynamics and kinetics is crucial in drug design. However, it remains challenging for conventional molecular dynamics (MD) simulations due to sampling issues. Gaussian accelerated MD (GaMD) is an enhanced sampling method that adds a harmonic boost to overcome energy barriers, which has demonstrated significant benefits in exploring protein-ligand interactions. Especially, the ligand GaMD (LiGaMD) applies a selective boost potential to the ligand nonbonded potential energy, significantly improving sampling for ligand binding and dissociation. Furthermore, a selective boost potential is applied to the potential of both ligand and protein residues around binding pocket in LiGaMD2 to further increase the sampling of protein-ligand interaction. LiGaMD and LiGaMD2 simulations could capture repetitive ligand binding and unbinding events within microsecond simulations, allowing to simultaneously characterize ligand binding thermodynamics and kinetics, which is expected to greatly facilitate drug design. In this chapter, we provide a brief review of the status of LiGaMD in drug discovery and outline its usage.
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