BetaSCP2: A program for the optimal prediction of side-chains in proteins
- Authors
- Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Song, Chanyoung; Kim, Deok-Soo
- Issue Date
- Aug-2014
- Publisher
- Springer Verlag
- Keywords
- beta-complex; BetaSCP2; protein structure/function; quasi-triangulation; side-chain prediction; Voronoi diagram
- Citation
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v.8592 LNCS, pp.333 - 340
- Indexed
- SCOPUS
- Journal Title
- Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
- Volume
- 8592 LNCS
- Start Page
- 333
- End Page
- 340
- URI
- https://scholarworks.bwise.kr/hanyang/handle/2021.sw.hanyang/159465
- DOI
- 10.1007/978-3-662-44199-2_52
- ISSN
- 0302-9743
- Abstract
- The side-chain prediction problem (SCP-problem), is a computational problem to predict the optimal structure of proteins by finding the optimal dihedral angles. The SCP-problem is one of key computational cornerstones for many important problems such as protein design, flexible docking of proteins, homology modeling, etc. The SCP-problem can be formulated as a minimization problem of an integer linear program which is NP-hard thus inevitably invites heuristic approach to find the solution. In this paper, we report a heuristic algorithm, called BetaSCP2, which quickly finds an excellent solution of the SCP-problem. The solution process of the BetaSCP2 is facilitated by the Voronoi diagram and its dual structure called the quasi-triangulation. The BetaSCP2 is entirely implemented using the Molecular Geometry engine called BULL! which has been developed by Voronoi Diagram Research Center (VDRC) in C++ programming language. The benchmark test of the BetaSCP2 with other programs is also provided. The BetaSCP2 program is available as both a stand-alone and a web server program from VDRC.
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