Fast detection of common geometric substructure in proteins

We consider the problem of identifying common three-dimensional substructures between proteins. Our method is based on comparing the shape of the α-carbon backbone structures of the proteins in order to find 3D rigid motions that bring portions of the geometric structures into correspondence. We propose a geometric representation of protein backbone chains that is compact yet allows for similarity measures that are robust against noise and outliers. We represent the structure of the backbone as a sequence of unit vectors, defined by each adjacent pair of α-carbons; we then define a measure of the similarity of two protein structures based on the RMS (root mean squared) distance between corresponding orientation vectors of the two proteins. Our measure has several advantages over measures that are commonly used for comparing protein shapes, such as the minimum RMS distance between the 3D positions of corresponding atoms in two proteins. This new measure behaves well for identifyin...

• Type: Conference
• Year: 1999
• Where: RECOMB
• Authors: L. Paul Chew, Daniel P. Huttenlocher, Klara Kedem, Jon M. Kleinberg
• Keywords: Common Three-dimensional Substructures, Computational Biology, Protein, Protein Backbone Chains, RECOMB 1999