Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

ABSTRACT: Typically, the ensemble average polar component of solvation energy (ΔG_polar^solv) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG_polar^solv) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG_polar

SUBMITTER: Chakravorty A 

PROVIDER: S-EPMC9885857 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature