Exploring the binding mechanism of a small molecular Hsp70-Bim PPI inhibitor through molecular dynamic simulation.

Xin LiYuying WangMaojun JiangFangkui YinHong ZhangLinjie YuanJingjing LiuXingyu WangZiqian WangZhichao Zhang

Published in: Journal of molecular modeling (2024)

The binding mechanism of S1g-6 and Hsp70 was predicted through the molecular dynamics (MD) method by Gromacs-2021.3. The MD simulation was performed with 100-ps NVT and 100-ps NPT ensemble, and the force field was chosen as the Charmm36 force field. The temperature was set as 300 K, the time step was 2 fs and the total MD simulation time was 500 ns.

Keyphrases

molecular dynamics
single molecule
density functional theory
heat shock protein
heat shock
heat stress
dna binding
binding protein
machine learning
zika virus