Structure alignment based on coding of local geometric measures

Background: A structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to anothe...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Peter L. Chang, Andrew W. Rinne, T. Gregory Dewey
• Keywords: BMCBI 2006, Sequence Alignment, Structure Alignment, Writhing Number