Patent ID: 8589137
Filing Date: 2013-11-19
Classification: G16C

Abstract:
1. A method for performing a molecular dynamics simulation for determining the solvent accessible surface area of a molecule (M) with respect to atomic coordinates, the molecule (M) comprising a plurality of atoms, a sphere (B i ) being assigned to each atom, and each sphere (B i ) comprising a radius (ρ i ) and a center position (r i ) the method comprising: determining, by a computer, for each sphere (B) all neighbouring spheres (B defining, by the computer, a set of one or more contours (C determining, by the computer, for each contour (C determining, by the computer, the solvent accessible surface (S) of said sphere (B) as the surface of said sphere (B) subtracted by the area comprised by all contours (C determining, by the computer, the solvent accessible surface area of the molecule (M) based on a sum of solvent accessible surface areas (S determining, by the computer, the derivative of the solvent accessible surface area (S) of said sphere (B) with respect to the position (r i ) of the intersecting spheres (B i ) satisfying the formula: wherein S is the solvent accessible surface area of said sphere (B); r ρ is the radius of said sphere (B); ρ b e ν