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Integer Programming Approach to HP Folding

Yanev, N.Milanov, PeterMirchev, I. — 2011

Serdica Journal of Computing

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...

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