Paper by Erik D. Demaine

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.

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.

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

The paper is 27 pages.

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

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Last updated March 9, 2018 by Erik Demaine.