Fast solvent-accessible surface generation algorithm based on iso-contouring

Description of molecular shape plays an important role in the analysis of protein-protein and protein-ligand interactions. By means of iso-surface theory, this paper proposes a molecular solvent-accessible surface generation program and makes the corresponding efficiency tests. The proposed method adopts a rapid one dimensional recursive Gaussian filter algorithm, in which the iso-surface is constructed in the discrete three dimensional spaces and the molecular solvent-accessible surface of triangle representations by using iso-surface extraction technique " Marching Cubes". Moreover, the central difference method is utilized to calculate the normal vector of triangles such that a better render effect is achieved. The experimental results show that the present method has faster speed and higher accuracy of computation, and can provide effective drug target surface representations for structure-based target identifications. Now, this proposed program has been integrated into the software package, D³ Pharma.