A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry.

ABSTRACT: A novel grid-based method is presented, which in conjunction with a smooth Gaussian-based model of atoms, is used to compute molecular volume (MV) and surface area (MSA). The MV and MSA are essential for computing nonpolar component of free energies. The objective of our grid-based approach is to identify solute atom pairs that share overlapping volumes in space. Once completed, this information is used to construct a rooted tree using depth-first method to yield the final volume and SA by using the formulations of the Gaussian model described by Grant and Pickup (J. Phys Chem, 1995, 99, 3503). The method is designed to function uninterruptedly with the grid-based finite-difference method implemented in Delphi, a popular and open-source package used for solving the Poisson-Boltzmann equati

SUBMITTER: Chakravorty A 

PROVIDER: S-EPMC6506848 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature