ArticleJournal of chemical theory and computation2024
Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Artificial intelligence and ultra-high performance computing methods and experiments for drug discovery: virtual screening, deep learning, molecular dynamics simulations, ADMET modelling, and experimental validation.Molecular biomedicine · 2026Review
- New paradigm of q-CAR drug development targeting disease-specific protein conformations.npj drug discovery · 2026Review
- ModBindProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Ligand-mediated conformation diversity of Hsp90 revealed by GaMD simulations and Markov model.Molecular diversity · 2026Article
- Structural insights into single-pass transmembrane receptor GC-A activation by distinct antihypertensive antibodies.Nature communications · 2026Article
- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
- Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation.Journal of chemical information and modeling · 2025Article
- Systematic Search for Blood-Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain-Domain Docking.Journal of chemical information and modeling · 2025Article
- 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
- Diverse toxins exhibit a common binding mode to the nicotinic acetylcholine receptors.Biophysical journal · 2025Article
- Identifying Inhibitor-SARS-CoV2-3CLMolecules (Basel, Switzerland) · 2025Article
- ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates.Journal of chemical information and modeling · 2025Article
- Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics.Journal of chemical theory and computation · 2024Article
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Abstract
Binding thermodynamics and kinetics play critical roles in drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics of small molecules and flexible peptides using conventional molecular dynamics (cMD), due to limited simulation time scales. Based on our previously developed ligand Gaussian accelerated molecular dynamics (LiGaMD) method, we present a new approach, termed "LiGaMD3″, in which we introduce triple boosts into three individual energy terms that play important roles in small-molecule/peptide dissociation, rebinding, and system conformational changes to improve the sampling efficiency of small-molecule/peptide interactions with target proteins. To validate the performance of LiGaMD3, MDM2 bound by a small molecule (Nutlin 3) and two highly flexible peptides (PMI and P53) were chosen as the model systems. LiGaMD3 could efficiently capture repetitive small-molecule/peptide dissociation and binding events within 2 μs simulations. The predicted binding kinetic constant rates and free energies from LiGaMD3 were in agreement with the available experimental values and previous simulation results. Therefore, LiGaMD3 provides a more general and efficient approach to capture dissociation and binding of both small-molecule ligands and flexible peptides, allowing for accurate prediction of their binding thermodynamics and kinetics.
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