%0 Journal Article
%T Structural pattern matching of nonribosomal peptides
%A S¨¦gol¨¨ne Caboche
%A Maude Pupin
%A Val¨¦rie Lecl¨¨re
%A Phillipe Jacques
%A Gregory Kucherov
%J BMC Structural Biology
%D 2009
%I BioMed Central
%R 10.1186/1472-6807-9-15
%X 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.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.Nonribosomal Peptides (NRPs) are bioactive compounds having various important biological functions (e.g. as antibiotics, siderophores, antitumor agents, immunosuppressants). NRPs are synthesized by large multi-enzymatic complexes called Nonribosomal Peptide Synthetases (NRPSs) that are modularly organized [1]. Each module is responsible for the incorporation of a specific monomer and is itself subdivided into domains catalysing specific enzymatic reactions.Until about fifteen years ago, the number of known NRPs remained relatively low. However, many new molecules have been reported in the literature during the last years, associated with different biological activities and having a broad range of potential applications. This triggered a considerable interest among the research community in the nonribosomal synthesis pathway.Among potential applications of such studies, redesigning natural products by genetic engineering of NRPSs opens an interesting new way in drug discovery [2]. Indeed, modifying the nucleotide sequence of a natural NRPS or combining modules of different NRPSs could potentially yield a more efficient compound or a product with a new biological activity. However, generating a new peptide with a specific function from a modified NRPS nucleic sequence requires a deep understanding of both the assembly line and the resulting products.NRPS enzymes have been well studied for several years. Stachelhau
%U http://www.biomedcentral.com/1472-6807/9/15