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.

BibTeX

@Article{RedBlue_CGTA2003,
  AUTHOR        = {Oswin Aichholzer and David Bremner and Erik D. Demaine and
                   Henk Meijer and Vera Sacrist\'an and Michael Soss},
  TITLE         = {Long Proteins with Unique Optimal Foldings in the {H-P} Model},
  JOURNAL       = {Computational Geometry: Theory and Applications},
  journalurl    = {https://www.sciencedirect.com/journal/computational-geometry},
  VOLUME        = 25,
  NUMBER        = {1--2},
  MONTH         = {May},
  YEAR          = {2003},
  PAGES         = {139--159},
  NOTE          = {Special issue of selected papers from the 17th European
                   Workshop on Computational Geometry, 2001.},

  length        = {27 pages},
  papers        = {EuroCG2001},
  replaces      = {EuroCG2001},
  doi           = {https://dx.doi.org/10.1016/S0925-7721(02)00134-7},
  dblp          = {https://dblp.org/rec/journals/comgeo/AichholzerBDMSS03},
  comments      = {This paper is also available from the
                   <A HREF="http://dx.doi.org/10.1016/S0925-7721(02)00134-7">ScienceDirect</A>.
                   <P>
                   This paper is also available as
                   <A HREF="http://arXiv.org/abs/cs.CG/0201018">
                   arXiv:cs.CG/0201018</A> of the
                   <A HREF="http://arXiv.org/archive/cs/intro.html">
                   Computing Research Repository (CoRR)</A>.},
}

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.

Availability:

The paper is available in PostScript (543k), gzipped PostScript (112k), and PDF (235k).

See information on file formats.

[Google Scholar search]

Related papers:

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