Paper by Erik D. Demaine

Reference:

Oswin Aichholzer, David Bremner, Erik D. Demaine, Henk Meijer, Vera Sacristán, and Michael Soss, “Long Proteins with Unique Optimal Foldings in the H-P Model”, Computational Geometry: Theory and Applications, volume 25, number 1–2, May 2003, pages 139–159. Special issue of selected papers from the 17th European Workshop on Computational Geometry, 2001.

Abstract:

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process. In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings? In particular, we prove that there are closed chains of monomers (amino acids) with this property for all (even) lengths; and that there are open monomer chains with this property for all lengths divisible by four.

Comments:

This paper is also available from the ScienceDirect.

This paper is also available as arXiv:cs.CG/0201018 of the Computing Research Repository (CoRR).

Length:

The paper is 27 pages.

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Related papers:

EuroCG2001 (Long Proteins with Unique Optimal Foldings in the H-P Model)