Geometric modeling applications in rational drug design: a survey
Computer aided design methods are starting to gain acceptance in the field of life sciences and drug discovery, thus giving rise to a discipline coined Computer Aided Drug Discovery (CADD). This trend is accompanied by a larger interest in 3-dimensional ...
Segmenting molecular surfaces
This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of ...
Quality meshing of implicit solvation models of biomolecular structures
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 ...
Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials
Distance-dependent, pairwise, statistical potentials are based on the concept that the packing observed in known protein structures can be used as a reference for comparing different 3D models for a protein. Here, packing refers to the set of all pairs ...
Geometry-guided computation of 3D electrostatics for large biomolecules
Electrostatic interactions play a central role in biological processes. Development of fast computational methods to solve the underlying Poisson-Boltzmann equation (PBE) is vital for biomolecular modeling and simulation package. In this paper, we ...
