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Knot Invariants in Protein Structure Comparison
by
Elena Zotenko
NIH/NLM/NCBI and University of Maryland College Park
Coauthors: Teresa M. Przytycka (NIH/NLM/NCBI)
Given a query protein the ability to identify all structurally similar proteins is of primary importance in the study of protein evolution and function. As the number of protein structures grows there is a need to develop screening methods that will perform quick yet accurate filtering of the database before a more computationally expensive protein structure comparison method is applied.
Our long term goal is to develop such screening method for VAST (Vector Alignment Search Tool), a protein structure comparison method used at NCBI. Average crossing number, a geometric invariant based on the writhing number of a knot, was used by several researchers to provide a global descriptor of protein shape [1, 2]. We suggest a screening method that uses average crossing number to detect locally similar substructures. Local similarities are then efficiently combined to detect similar protein structures.
In this talk I will give an overview of protein structure comparison problem and previous work on using average crossing number to compare protein structures. Then I will describe our screening method and the ability of average crossing number to detect locally similar substructures.
References:
[1] G.A. Arteca and O. Tapia. Characterization of fold diversity among proteins with the same number of amino acid residues. J.Chem.Inf.Comput.Sci., 39:642649, 1999.
[2] P. Rogen and B. Henrik. A new family of global protein shape descriptors. Mathematical Biosciences, 182:167181, 2003.
Date received: October 11, 2004
Copyright © 2004 by the author(s). The author(s) of this work and the organizers of the conference have granted their consent to include this abstract in Topology Atlas. Document # capf-05.