Protein Folding on Lattices: An Integer Programming Approach

16 Pages Posted: 1 Oct 2012

See all articles by Vijay Chandru

Vijay Chandru

Indian Institute of Science (IISc)

M. Rao

Indian Institute of Management (IIMB), Bangalore

Ganesh Swaminathan

Strand Life Sciences

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

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

Vijay Chandru

Indian Institute of Science (IISc) ( email )

IN
India

M. Rao (Contact Author)

Indian Institute of Management (IIMB), Bangalore ( email )

Bannerghatta Road
Bangalore, Karnataka 560076
India

Ganesh Swaminathan

Strand Life Sciences ( email )

5th Floor, Kirloskar Business Park
Bellary Road, Hebbal
Bangalore, 560024
India

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