Geodesic
Integer Programming Approach to HP Folding
Serdica Journal of Computing, Tome 5 (2011) no. 4, pp. 359-366.

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One of the most widely studied protein structure prediction models is the hydrophobic-hydrophilic (HP) model, which explains the hydrophobic interaction and tries to maximize the number of contacts among hydrophobic amino-acids. In order to find a lower bound for the number of contacts, a number of heuristics have been proposed, but finding the optimal solution is still a challenge. In this research, we focus on creating a new integer programming model which is capable to provide tractable input for mixed-integer programming solvers, is general enough and allows relaxation with provable good upper bounds. Computational experiments using benchmark problems show that our formulation achieves these goals.
Keywords: Protein Folding, HP Model, Integer Programming 
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     author = {Yanev, N. and Milanov, Peter and Mirchev, I.},
     title = {Integer {Programming} {Approach} to {HP} {Folding}},
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Yanev, N.; Milanov, Peter; Mirchev, I. Integer Programming Approach to HP Folding. Serdica Journal of Computing, Tome 5 (2011) no. 4, pp. 359-366. http://geodesic.mathdoc.fr/item/SJC_2011_5_4_a3/