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. © 2014 Springer-Verlag.
CITATION STYLE
Ryu, J., Lee, M., Cha, J., Song, C., & Kim, D. S. (2014). BetaSCP2: A program for the optimal prediction of side-chains in proteins. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8592 LNCS, pp. 333–340). Springer Verlag. https://doi.org/10.1007/978-3-662-44199-2_52
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