Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.

ABSTRACT: Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol in

SUBMITTER: Koehl P 

PROVIDER: S-EPMC9930125 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature