BetaMol: A Molecular Modeling, Analysis and Visualization Software Based on the Beta-Complex and the Quasi-Triangulation

Abstract

Molecular shape is one of the most critical factors that determines molecular function. Therefore, it is frequently desirable to understand geometric characteristics of a molecule more precisely and efficiently. In this paper, we introduce the BetaMol, a molecular modeling, analysis, and visualization software based on the recent theory of the beta-complex and the quasi-triangulation that are derived from the Voronoi diagram of three-dimensional spherical atoms. The powerful features of the BetaMol are solely based on a unified, single framework of the mathematically rigorous and computationally efficient beta-complex theory. The BetaMol is implemented in the standard C++ language with OpenGL graphics library and freely available at Voronoi Diagram Research Center web site (http://voronoi.hanyang.ac.kr).

Keywords

• voronoi diagram
• quasi-triangulation
• beta-shape
• beta-complex
• molecular modeling
• molecular visualization
• software
• computational molecular biology
• structural molecular biology