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Open Access Methodology article

Structural pattern matching of nonribosomal peptides

Ségolène Caboche12*, Maude Pupin1, Valérie Leclère2, Phillipe Jacques2 and Gregory Kucherov1

Author Affiliations

1 Computer Science Laboratory of Lille, UMR USTL/CNRS 8022, INRIA, F59655, Villeneuve d'Ascq, France

2 ProBioGEM (UPRES EA 1026), University of Sciences and Technologies of Lille, F59655, Villeneuve d'Ascq, France

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BMC Structural Biology 2009, 9:15  doi:10.1186/1472-6807-9-15

Published: 18 March 2009

Abstract

Background

Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database.

Results

We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph.

Conclusion

The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine webcite. Less than one second is needed to search for a pattern in the entire database.