BetaSuperposer: superposition of protein surfaces using beta-shapes
- Title
- BetaSuperposer: superposition of protein surfaces using beta-shapes
- Author
- 김덕수
- Keywords
- molecule structure; molecule superposition; molecule structure alignment; Voronoi diagram; beta-complex; beta-shape; PDB
- Issue Date
- 2012-07
- Publisher
- Taylor & Francis INC
- Citation
- Journal of Biomolecular Structure and Dynamics, 2012, 30(6), P.684-700
- Abstract
- The comparison between two protein structures is important for understanding a molecular function. In particular, the comparison of protein surfaces to measure their similarity provides another challenge useful for studying molecular evolution, docking, and drug design. This paper presents an algorithm, called the BetaSuperposer, which evaluates the similarity between the surfaces of two structures using the beta-shape which is a geometric structure derived from the Voronoi diagram of molecule. The algorithm performs iterations of mix-and-match between the beta-shapes of two structures for the optimal superposition from which a similarity measure is computed, where each mix-and-match step attempts to solve an NP-hard problem. The devised heuristic algorithm based on the assignment problem formulation quickly produces a good superposition and an assessment of similarity. The BetaSuperposer was fully implemented and benchmarked against popular programs, the Dali and the Click, using the SCOP models. The BetaSuperposer is freely available to the public from the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr).
- URI
- https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.689700https://repository.hanyang.ac.kr/handle/20.500.11754/73029
- ISSN
- 0739-1102; 1538-0254
- DOI
- 10.1080/07391102.2012.689700
- Appears in Collections:
- COLLEGE OF ENGINEERING[S](공과대학) > MECHANICAL ENGINEERING(기계공학부) > Articles
- Files in This Item:
There are no files associated with this item.
- Export
- RIS (EndNote)
- XLS (Excel)
- XML