Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.

ABSTRACT: We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational implicit-solvent model (VISM), and a binary level-set method for the simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the biomolecular complex is estimated by minimizing the VISM free-energy functional of all possible solute-solvent interfaces that are used as dielectric boundaries. This functional consists of the solute volumetric, solute-solvent interfacial, solute-solvent van der Waals interaction, and electrostatic free energy. A technique of shifting the dielectric boundary is used to accurately predict the electrostatic part of the solvation free energy. Minimizing such a functional in each MC move is made possible by our new and fast binary level-set method. T

SUBMITTER: Zhang Z 

PROVIDER: S-EPMC8817676 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature