Solving and analyzing side-chain positioning problems using linear and integer programming | Zendy

Carleton L. Kingsford | Zendy; Bernard Chazelle | Zendy; Mona Singh | Zendy

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Solving and analyzing side-chain positioning problems using linear and integer programming

Author(s) -

Carleton L. Kingsford,

Bernard Chazelle,

Mona Singh

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti144

Subject(s) - integer programming , computer science , integer (computer science) , linear programming , mathematical optimization , chain (unit) , algorithm , mathematics , programming language , physics , astronomy

Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optimized. It is NP-complete to find even a reasonable approximate solution to this problem. We seek to put this hardness result into practical context.

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