Molecular Surface Estimation by Geometric Coupled Distance Functions

Abstract

Estimating the surface from given atoms with location and size information is a fundamental task in many fields, such as molecular dynamics and protein analysis. In this paper, we present a novel method for such surface estimation. Our method is based on level set representations, which can efficiently handle complex geometries. The proposed method is analyzed from mathematical point of view and from computation point of view. The method does not require any prior information about the surface. This property is fundamentally important for the surface estimation task. The presented method is evaluated on both synthetic and real data. Several numerical experiments confirm that our method is effective and computationally efficient. Finally, the method is applied on protein surface estimation. This method is suitable for high performance molecular dynamics study, protein surface analysis, etc.

Keywords

• Molecule
• surface
• level set
• mean curvature