Title :
Protein Structural Domain Assignment with a Delaunay Tessellation Derived Lattice
Author :
Taylor, Todd J. ; Vaisman, Iosif I.
Author_Institution :
Sch. of Comput. Sci., George Mason Univ., Manassas, VA
Abstract :
We describe a fully automated method of protein structural domain assignment using a Potts model which we call DePot (an abbreviation for Delaunay-Potts). It is a heavily modified version of a method described previously by WR Taylor. Each amino acid residue is represented as a site in an irregular lattice derived from the Delaunay tessellation of the protein structure. Domain membership is represented by a spin value and each site has a spin which can change under the influence of its neighbors. Spins are allowed to interact subject to an Ising ferromagnetic-like energy function until clusters of like spins emerge and these clusters define domains. DePot is simple and easy to implement and the assignments agree well with previously published methods.
Keywords :
Potts model; biology computing; biomagnetism; mesh generation; molecular biophysics; molecular configurations; proteins; Delaunay tessellation derived lattice; Ising ferromagnetic-like energy function; Potts model; amino acid residue; protein structural domain assignment; spin value; Amino acids; Bonding; Chemicals; Coils; Decision support systems; Lattices; Nitrogen; Proteins; Sequences; Shape;
Conference_Titel :
Voronoi Diagrams in Science and Engineering, 2006. ISVD '06. 3rd International Symposium on
Conference_Location :
Banff, Alberta, BC
Print_ISBN :
0-7695-2630-6
DOI :
10.1109/ISVD.2006.29