Structural pattern matching of nonribosomal peptides.

Abstract : 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. 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.
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Ségolène Caboche, Maude Pupin, Valérie Leclère, Philippe Jacques, Gregory Kucherov. Structural pattern matching of nonribosomal peptides.. BMC Structural Biology, BioMed Central, 2009, 9 (15), ⟨10.1186/1472-6807-9-15⟩. ⟨hal-00641486⟩

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