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Please use this identifier to cite or link to this item: http://hdl.handle.net/10525/1633

Title: Integer Programming Approach to HP Folding
Authors: Yanev, N.
Milanov, Peter
Mirchev, I.
Keywords: Protein Folding
HP Model
Integer Programming
Issue Date: 2011
Publisher: Institute of Mathematics and Informatics Bulgarian Academy of Sciences
Citation: Serdica Journal of Computing, Vol. 5, No 4, (2011), 359p-366p
Abstract: 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.
URI: http://hdl.handle.net/10525/1633
ISSN: 1312-6555
Appears in Collections:Volume 5 Number 4

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