Quality Meshing of Implicit Solvation Models of Biomolecular Structures.

ABSTRACT: This paper describes a comprehensive approach to construct quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). First, a smooth volumetric electron density map is constructed from atomic data using weighted Gaussian isotropic kernel functions and a two-level clustering technique. This enables the selection of a smooth implicit solvation surface approximation to the Lee-Richards molecular surface. Next, a modified dual contouring method is used to extract triangular meshes for the surface, and tetrahedral meshes for the volume inside or outside the molecule within a bounding sphere/box of influence. Finally, geometric flow techniques are used to improve the surface and volume mesh quality. Several exampl

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC2756697 | biostudies-literature | 2006 Aug

REPOSITORIES: biostudies-literature