Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.

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 timescales. 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) a

SUBMITTER: Wang J 

PROVIDER: S-EPMC11100592 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature