Tunnels and Voids in Molecules via Voronoi Diagrams and Beta-complexes
- Title
- Tunnels and Voids in Molecules via Voronoi Diagrams and Beta-complexes
- Author
- 김덕수
- Keywords
- Voronoi diagram of spheres; quasi-triangulation; van der Waals region; simplexes; bounding state; simplicial complex; union of spheres; union of disks; molecular structure; external structure; beta-shape; beta-complex
- Issue Date
- 2013-08
- Publisher
- SPRINGER-VERLAG
- Citation
- Lecture Notes in Computer Science, 2013, 8110, P.92-111
- Abstract
- Molecular external structure is important in understanding molecular interaction with its solvent environment and is useful in developing drugs. Important examples of external structures are tunnels, pockets, caves, clefts, voids, etc. This paper presents algorithms to extract tunnels and voids from molecular structures. The algorithms are based on the the Voronoi diagram of atoms in molecules and their time complexity are both O(m) time in the worst case, where m represents the number of entities in the Voronoi diagram. The algorithms are mathematically correct, computationally efficient, numerically robust, and easy to implement.
- URI
- https://link.springer.com/chapter/10.1007%2F978-3-642-41905-8_7http://hdl.handle.net/20.500.11754/52499
- ISSN
- 0302-9743
- DOI
- 10.1007/978-3-642-41905-8_7
- Appears in Collections:
- COLLEGE OF ENGINEERING[S](공과대학) > MECHANICAL ENGINEERING(기계공학부) > Articles
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