Protein Structural Domain Assignment with a Delaunay Tessellation Derived Lattice

摘要

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.