Voronoi Tesselations of Proteins for Computing Contact Maps

Authors: 

Gregory Zaverucha

Author Addresses: 

Faculty of Computer Science
Dalhousie University
6050 University Ave.
PO Box 15000
Halifax, Nova Scotia, Canada
B3H 4R2

Abstract: 

This paper examines the use of Voronoi tessellations of proteins for generating contact maps, and compares it to existing methods. A Voronoi tesselation is computed on the three dimensional protein data, with each amino acid as a site. If two reigions in the Voronoi tesselation share a face, then the amino acids that created the regions are considered in contact. Amino acids are represented by points at their geometric centers. A simple cutoff method will be used for comparison. The results show that the Voronoi tessellation method can produce accurate, unambiguous contact maps. The new maps have on average 30\% fewer contacts, yet retain the patterns found on the maps produced by the cutoff method. More importantly, the data allowed us to tune the cutoff distance used in the reference method, justifying the choice of this parameter.

Tech Report Number: 
CS-2005-07
Report Date: 
June 27, 2005
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