ArticleJournal of chemical theory and computation2023
Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Design, synthesis and anti-glioblastoma multiforme activity of N-methoxy-2-(pyrimidin-4-ylamino)benzamide derivatives as focal adhesion kinase inhibitors.Molecular diversity · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Conformational Preferences for N-Glycans at the Surface of CEACAM1-Ig1.ACS chemical biology · 2026Article
- Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation.Journal of chemical information and modeling · 2025Article
- Conformational Heterogeneity Underlying Divergent Signaling in Class A G Protein-Coupled Receptors.ACS pharmacology & translational science · 2025Review
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics.The journal of physical chemistry letters · 2025Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo.Nature communications · 2025Article
- Diverse toxins exhibit a common binding mode to the nicotinic acetylcholine receptors.Biophysical journal · 2025Article
- Identifying Inhibitor-SARS-CoV2-3CLMolecules (Basel, Switzerland) · 2025Article
- Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0].Living journal of computational molecular science · 2025Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Molecular Mechanisms of the Impaired Heparin Pentasaccharide Interactions in 10 Antithrombin Heparin Binding Site Mutants Revealed by Enhanced Sampling Molecular Dynamics.Biomolecules · 2024Article
- Understanding the impact of binding free energy and kinetics calculations in modern drug discovery.Expert opinion on drug discovery · 2024Review
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Mechanism of Ligand Binding to Theophylline RNA Aptamer.Journal of chemical information and modeling · 2024Article
- Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics.Molecules (Basel, Switzerland) · 2024Article
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Abstract
Ligand binding thermodynamics and kinetics are critical parameters for drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics from molecular simulations due to limited simulation timescales. Protein dynamics, especially in the ligand binding pocket, often plays an important role in ligand binding. Based on our previously developed Ligand Gaussian accelerated molecular dynamics (LiGaMD), here we present LiGaMD2 in which a selective boost potential was applied to both the ligand and protein residues in the binding pocket to improve sampling of ligand binding and dissociation. To validate the performance of LiGaMD2, the T4 lysozyme (T4L) mutants with open and closed pockets bound by different ligands were chosen as model systems. LiGaMD2 could efficiently capture repetitive ligand dissociation and binding within microsecond simulations of all T4L systems. The obtained ligand binding kinetic rates and free energies agreed well with available experimental values and previous modeling results. Therefore, LiGaMD2 provides an improved approach to sample opening of closed protein pockets for ligand dissociation and binding, thereby allowing for efficient calculations of ligand binding thermodynamics and kinetics.
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