Integer Programming Approach to HP Folding

Yanev, N., Milanov, Peter, and Mirchev, I.. "Integer Programming Approach to HP Folding." Serdica Journal of Computing 5.4 (2011): 359-366. <http://eudml.org/doc/219645>.

@article{Yanev2011,
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.This work was supported by NFSR of Bulgaria, projects DOO2-162/16.12.2008, DOO2-135/31.07.2009 and DO 02-359},
author = {Yanev, N., Milanov, Peter, Mirchev, I.},
journal = {Serdica Journal of Computing},
keywords = {Protein Folding; HP Model; Integer Programming},
language = {eng},
number = {4},
pages = {359-366},
publisher = {Institute of Mathematics and Informatics Bulgarian Academy of Sciences},
title = {Integer Programming Approach to HP Folding},
url = {http://eudml.org/doc/219645},
volume = {5},
year = {2011},
}

TY - JOUR
AU - Yanev, N.
AU - Milanov, Peter
AU - Mirchev, I.
TI - Integer Programming Approach to HP Folding
JO - Serdica Journal of Computing
PY - 2011
PB - Institute of Mathematics and Informatics Bulgarian Academy of Sciences
VL - 5
IS - 4
SP - 359
EP - 366
AB - 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.This work was supported by NFSR of Bulgaria, projects DOO2-162/16.12.2008, DOO2-135/31.07.2009 and DO 02-359
LA - eng
KW - Protein Folding; HP Model; Integer Programming
UR - http://eudml.org/doc/219645
ER -