Protein Folding on Lattices: An Integer Programming Approach
16 Pages Posted: 1 Oct 2012
Date Written: September 24, 2002
Abstract
In this paper, we initiate the study of the protein folding problem from an integer linear programming perspective. The particular variant of protein folding that we examine is known as the hydrophobic-hydrophilic (HP) model of protein folding on the integer lattice. This problem is known to be NP-hard and also maxSNP-hard. We examine various alternate formulations for the planar version of this problem and present some preliminary computational results. Hopefully, this sets the stage for a polyhedral combinatorics assault on this important problem.
Suggested Citation: Suggested Citation
Chandru, Vijay and Rao, M. and Swaminathan, Ganesh, Protein Folding on Lattices: An Integer Programming Approach (September 24, 2002). IIM Bangalore Research Paper No. 199, Available at SSRN: https://ssrn.com/abstract=2154543 or http://dx.doi.org/10.2139/ssrn.2154543
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