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BetaSuperposer: superposition of protein surfaces using beta-shapes

Title
BetaSuperposer: superposition of protein surfaces using beta-shapes
Author
김재관
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/20.500.11754/73030
ISSN
0739-1102; 1538-0254
DOI
10.1080/07391102.2012.689700
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ETC[S] > 연구정보
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