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Algorithms 2009, 2(1), 498-517; doi:10.3390/a2010498
Article

A Novel Algorithm for Macromolecular Epitope Matching

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Received: 27 October 2008 / Revised: 11 January 2009 / Accepted: 25 February 2009 / Published: 11 March 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
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Abstract

Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database.
Keywords: molecular similarity; matching algorithms; epitopes; molecular sub-structures; maximum common subgraph molecular similarity; matching algorithms; epitopes; molecular sub-structures; maximum common subgraph
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Jakuschev, S.; Hoffmann, D. A Novel Algorithm for Macromolecular Epitope Matching. Algorithms 2009, 2, 498-517.

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