BetaSCP2: A Program for the Optimal Prediction of Side-Chains in Proteins
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- 作者：Joonghyun Ryu (17)
Mokwon Lee (17)
Jehyun Cha (17)
Chanyoung Song (17)
Deok-Soo Kim (18) - 关键词：protein structure/function ; side ; chain prediction ; BetaSCP2 ; Voronoi diagram ; quasi ; triangulation ; beta ; complex
- 刊名：Lecture Notes in Computer Science
- 出版年：2014
- 出版时间：2014
- 年：2014
- 卷：8592
- 期：1
- 页码：333-340
- 全文大小：936 KB
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Mokwon Lee (17)
Jehyun Cha (17)
Chanyoung Song (17)
Deok-Soo Kim (18)
17. Voronoi Diagram Research Center, Hanyang Univeristy, South Korea
18. Hanyang Univeristy, South Korea - ISSN：1611-3349
文摘
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.