A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.

ABSTRACT: Ligand-receptor docking simulation is difficult when the biomolecules have high intrinsic flexibility. If some knowledge on the ligand-receptor complex structure or inter-molecular contact sites are presented in advance, the difficulty of docking problem considerably decreases. This paper proposes a generalized-ensemble method "cartesian-space division mD-VcMD" (or CSD-mD-VcMD), which calculates stable complex structures without assist of experimental knowledge on the complex structure. This method is an extension of our previous method that requires the knowledge on the ligand-receptor complex structure in advance. Both the present and previous methods enhance the conformational sampling, and finally produce a binding free-energy landscape starting from a completely dissociated conformati

SUBMITTER: Higo J 

PROVIDER: S-EPMC12151736 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature