Name
Abstract | ||
|---|---|---|
It has been generally accepted that the structure of molecule is one of the most important factors which determine the functions of a molecule. Hence, studies have been conducted to analyze the structure of a molecule. Molecular surface is an important example of molecular structure. Given a molecular surface, the area and volume of the molecule can be computed to facilitate problems such as protein docking and folding. Therefore, it is important to compute a molecular surface precisely and efficiently. This paper presents an algorithm for correctly and efficiently computing the blending surfaces of a protein which is an important part of the molecular surface. Assuming that the Voronoi diagram of atoms of a protein is given, we first compute the beta-shape of the protein corresponding to a solvent probe. Then, we use a search space reduction technique for the intersection tests while the link blending surface is computed. Once a beta-shape is obtained, the blending surfaces corresponding to a given solvent probe can be computed in O(n) in the worst case, where n is the number of atoms. The correctness and efficiency of the algorithm stem from the powerful properties of beta-shape, quasi-triangulation, and the interworld data structure. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1109/ISVD.2007.1 | ISVD |
Keywords | Field | DocType |
fundamental geometric problem,voronoi diagram,blending surfaces,protein folding,molecular structure,well-known conjecture,molecular surface,euclidean space,computational geometry,proteins,data structure,search problems,biology computing,molecular biophysics,computational complexity,finite system,beta-shape based computation,quasitriangulation,search space reduction,finite set,protein docking,data structures,search space,electrostatics,surface topography,spline,protein engineering,testing | Data structure,Protein folding,Biological system,Molecule,Computational geometry,Theoretical computer science,Macromolecular docking,Voronoi diagram,Molecular biophysics,Mathematics,Computation | Conference |
ISBN | Citations | PageRank |
0-7695-2869-4 | 3 | 0.41 |
References | Authors | |
10 | 5 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Joonghyun Ryu | 1 | 148 | 14.39 |
| Rhohun Park | 2 | 42 | 2.38 |
| Youngsong Cho | 3 | 250 | 22.15 |
| Jeongyeon Seo | 4 | 35 | 3.60 |
| Deok-Soo Kim | 5 | 633 | 59.12 |