title   
  

Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks

Yanıkoğlu, Berrin and Erman, Burak (2002) Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks. Journal of Computational Biology, 9 (4). pp. 613-620. ISSN 1066-5277

[img]PDF (This is a RoMEO blue journal -- author can archive publisher's version/PDF) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
150Kb

Official URL: http://dx.doi.org/10.1089/106652702760277345

Abstract

We use self-organizing maps (SOM) as an efficient tool to find the minimum energy configurations of the 2-dimensional HP-models of proteins. The usage of the SOM for the protein folding problem is similar to that for the Traveling Salesman Problem. The lattice nodes represent the cities whereas the neurons in the network represent the amino acids moving towards the closest cities, subject to the HH interactions. The valid path that maximizes the HH contacts corresponds to the minimum energy configuration of the protein. We report promising results for the cases when the protein completely fills a lattice and discuss the current problems and possible extensions. In all the test sequences up to 36 amino acids, the algorithm was able to find the global minimum and its degeneracies.

Item Type:Article
Uncontrolled Keywords:protein folding; structure prediction; self organizing maps
Subjects:UNSPECIFIED
ID Code:18836
Deposited By:Berrin Yanıkoğlu
Deposited On:17 Feb 2012 15:29
Last Modified:17 Feb 2012 15:29

Repository Staff Only: item control page