BetaSuperposer: superposition of protein surfaces using beta-shapes.
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 ).
Department of Industrial Engineering and Voronoi Diagram Research Center, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul, 133-791, South Korea.
Jae-Kwan
JK
Kim
Deok-Soo
DS
Kim
D000465:Algorithms; D000595:Amino Acid Sequence; D058833:Antithrombin Proteins / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017711:Nonlinear Dynamics; D017434:Protein Structure, Tertiary; D012044:Regression Analysis; D012984:Software; D040681:Structural Homology, Protein; D013499:Surface Properties
D058833:Antithrombin Proteins