05300503

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05300503 Ryu, Joonghyun Park, Rhohun Seo, Jeongyeon Kim, Chongmin Lee, Hyun Chan Kim, Deok-Soo Real-time triangulation of molecular surfaces. Gervasi, Osvaldo (ed.) et al., Computational science and its applications -- ICCSA 2007. International conference, Kuala Lumpur, Malaysia, August 26--29, 2007. Proceedings, Part I. Berlin: Springer (ISBN 978-3-540-74468-9/pbk). Lecture Notes in Computer Science 4705, 55-67 (2007). 2007 Berlin: Springer EN a protein a molecular surface $\beta $-shape a Voronoi diagram of atoms

doi:10.1007/978-3-540-74472-6_5

Summary: Protein consists of a set of atoms. Given a protein, the molecular surface of the protein is defined with respect to a probe approximating a solvent molecule. This paper presents an efficient, as efficient as the realtime, algorithm to triangulate the blending surfaces which is the most critical subset of a molecular surface. For the quick evaluation of points on the surface, the proposed algorithm uses masks which are similar in their concepts to those in subdivision surfaces. More fundamentally, the proposed algorithm takes advantage of the concise representation of topology among atoms stored in the $\beta $-shape which is indeed used in the computation of the blending surface itself. Given blending surfaces and the corresponding $\beta $-shape, the proposed algorithm triangulates the blending surfaces in $O(c \cdot m)$ time in the worst case, where $m$ is the number of boundary atoms in the protein and $c$ is the number of point evaluations on a patch in the blending surface.