김재관
2018-07-26T01:52:38Z
2018-07-26T01:52:38Z
2012-07
Journal of Biomolecular Structure and Dynamics, 2012, 30(6), P.684-700
0739-1102
1538-0254
https://www.tandfonline.com/doi/abs/10.1080/07391102.2012.689700
https://repository.hanyang.ac.kr/handle/20.500.11754/73030
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).
This work was supported by the National Research Lab grant funded by the Ministry of Education, Science, and Technology, Korea [No. 2011-0020410].
en
Taylor & Francis INC
molecule structure
molecule superposition
molecule structure alignment
Voronoi diagram
beta-complex
beta-shape
PDB
BetaSuperposer: superposition of protein surfaces using beta-shapes
Article
10.1080/07391102.2012.689700
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Kim, Jae-Kwan
Kim, Deok-Soo
2012204748
S
DIVISION OF INDUSTRIAL INFORMATION STUDIES[S]
DIVISION OF INDUSTRIAL INFORMATION STUDIES
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