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Bioinformatics Advance Access published online on October 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn518
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A novel method for comparing topological models of protein structures enhanced with ligand information

Mallika Veeramalai 1,2,* and David Gilbert 1

1Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, UK
2Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Dr. Mallika Veeramalai, E-mail: mallikav{at}burnham.org


  Abstract

We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs and between SSEs and ligands are described by incoming/outgoing arcs and ligand arcs respectively; and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model (Gilbert, et al., 2000; Gilbert, et al., 2001; Viksna and Gilbert, 2001). Our TOPS+ strings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of NP-completeness associated with graph problems.

Our structure comparison method is computationally more efficient in identifying distantly related proteins than BLAST, CLUSTALW, SSAP and TOPS because of the compact and abstract string-based representation of protein structure which records both topological and biochemical information including the functionally important loop regions of the protein structures. The accuracy of our comparison method is comparable with that of TOPS. Also, we have demonstrated that our TOPS+ strings method out-performs the TOPS method for the ligand-dependent protein structures and provides biologically meaningful results.

Availability: The TOPS+ strings comparison server is available from http://www.dcs.gla.ac.uk/~mallika/topsplus.html.

Contact: mallikav{at}burnham.org

Associate Editor: Prof. Anna Tramontano

Received on March 31, 2008; revised on September 29, 2008; accepted on October 4, 2008

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