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NORINE: a database of nonribosomal peptides.

Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G - Nucleic Acids Res. (2007)

Bottom Line: In recent years, NRPs attracted a lot of attention because of their biological activities and pharmacological properties (antibiotic, immunosuppressor, antitumor, etc.).However, few computational resources and tools dedicated to those peptides have been available so far.Norine is focused on NRPs and contains more than 700 entries.

View Article: PubMed Central - PubMed

Affiliation: Computer Science Laboratory of Lille (UMR USTL/CNRS 8022) and INRIA, and ProBioGEM (UPRES EA 1026), University of Sciences and Technologies of Lille, 59655 Villeneuve d'A;scq, France. caboche@lifl.fr

ABSTRACT
Norine is the first database entirely dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. It is performed by huge protein complexes called nonribosomal peptide synthetases (NRPSs). The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids. The primary structure of these peptides is not always linear but often more complex and may contain cycles and branchings. In recent years, NRPs attracted a lot of attention because of their biological activities and pharmacological properties (antibiotic, immunosuppressor, antitumor, etc.). However, few computational resources and tools dedicated to those peptides have been available so far. Norine is focused on NRPs and contains more than 700 entries. The database is freely accessible at http://bioinfo.lifl.fr/norine/. It provides a complete computational tool for systematic study of NRPs in numerous species, and as such, should permit to obtain a better knowledge of these metabolic products and underlying biological mechanisms, and ultimately to contribute to the redesigning of natural products in order to obtain new bioactive compounds for drug discovery.

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Example of structure-based search. Two search features are provided. The structure search looks up for a peptide having exactly the query structure. The structural pattern search looks up for the peptides containing the query pattern as a subgraph. The query pattern can contain joker or alternatively-labeled nodes (X and/). In both types of search, the query can be specified using either linear or graph representation. A link to the dedicated peptide structure editor (in green) allows the user to automatically obtain the graph representation. Alternatively, the user can specify the query through the linear representation. In the last row, examples of resulting peptides are given.
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Figure 3: Example of structure-based search. Two search features are provided. The structure search looks up for a peptide having exactly the query structure. The structural pattern search looks up for the peptides containing the query pattern as a subgraph. The query pattern can contain joker or alternatively-labeled nodes (X and/). In both types of search, the query can be specified using either linear or graph representation. A link to the dedicated peptide structure editor (in green) allows the user to automatically obtain the graph representation. Alternatively, the user can specify the query through the linear representation. In the last row, examples of resulting peptides are given.

Mentions: The user can also search for a peptide by specifying its structure in the ‘structure-based search’ (Figure 3). The peptide structure can be specified using either a linear or a graph representation. A graph representation can be created using a dedicated structure editor integrated to Norine. The Norine editor is a Java applet that allows one to build quickly and easily a graph representation of a peptide, i.e. to specify monomers and links between them. Complex monomeric structures can be easily drawn with a friendly graphical interface: first, monomers are selected and corresponding graph nodes are created, which are then connected by drawing edges between the nodes. It is also possible to delete some monomers or the whole structure. The user can also open a text file generated by the visualization applet in order to modify the created graph by hand. Once the structure is completed, clicking the ‘go’ button returns the peptide structure to the appropriate field of the Norine search page and the search for it in the database can be launched right away. Both with the linear and graph representations, the user can specify either the entire peptide structure to look for, or a structural pattern that the peptide must contain. The containment is defined as the usual subgraph relation: a pattern occurs in a peptide if each node of the pattern labeled by a monomer can be associated to a node of the peptide labeled by the same monomer so that the linked (unlinked) nodes of the pattern are linked (respectively unlinked) in the peptide.Figure 3.


NORINE: a database of nonribosomal peptides.

Caboche S, Pupin M, Leclère V, Fontaine A, Jacques P, Kucherov G - Nucleic Acids Res. (2007)

Example of structure-based search. Two search features are provided. The structure search looks up for a peptide having exactly the query structure. The structural pattern search looks up for the peptides containing the query pattern as a subgraph. The query pattern can contain joker or alternatively-labeled nodes (X and/). In both types of search, the query can be specified using either linear or graph representation. A link to the dedicated peptide structure editor (in green) allows the user to automatically obtain the graph representation. Alternatively, the user can specify the query through the linear representation. In the last row, examples of resulting peptides are given.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238963&req=5

Figure 3: Example of structure-based search. Two search features are provided. The structure search looks up for a peptide having exactly the query structure. The structural pattern search looks up for the peptides containing the query pattern as a subgraph. The query pattern can contain joker or alternatively-labeled nodes (X and/). In both types of search, the query can be specified using either linear or graph representation. A link to the dedicated peptide structure editor (in green) allows the user to automatically obtain the graph representation. Alternatively, the user can specify the query through the linear representation. In the last row, examples of resulting peptides are given.
Mentions: The user can also search for a peptide by specifying its structure in the ‘structure-based search’ (Figure 3). The peptide structure can be specified using either a linear or a graph representation. A graph representation can be created using a dedicated structure editor integrated to Norine. The Norine editor is a Java applet that allows one to build quickly and easily a graph representation of a peptide, i.e. to specify monomers and links between them. Complex monomeric structures can be easily drawn with a friendly graphical interface: first, monomers are selected and corresponding graph nodes are created, which are then connected by drawing edges between the nodes. It is also possible to delete some monomers or the whole structure. The user can also open a text file generated by the visualization applet in order to modify the created graph by hand. Once the structure is completed, clicking the ‘go’ button returns the peptide structure to the appropriate field of the Norine search page and the search for it in the database can be launched right away. Both with the linear and graph representations, the user can specify either the entire peptide structure to look for, or a structural pattern that the peptide must contain. The containment is defined as the usual subgraph relation: a pattern occurs in a peptide if each node of the pattern labeled by a monomer can be associated to a node of the peptide labeled by the same monomer so that the linked (unlinked) nodes of the pattern are linked (respectively unlinked) in the peptide.Figure 3.

Bottom Line: In recent years, NRPs attracted a lot of attention because of their biological activities and pharmacological properties (antibiotic, immunosuppressor, antitumor, etc.).However, few computational resources and tools dedicated to those peptides have been available so far.Norine is focused on NRPs and contains more than 700 entries.

View Article: PubMed Central - PubMed

Affiliation: Computer Science Laboratory of Lille (UMR USTL/CNRS 8022) and INRIA, and ProBioGEM (UPRES EA 1026), University of Sciences and Technologies of Lille, 59655 Villeneuve d'A;scq, France. caboche@lifl.fr

ABSTRACT
Norine is the first database entirely dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. It is performed by huge protein complexes called nonribosomal peptide synthetases (NRPSs). The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids. The primary structure of these peptides is not always linear but often more complex and may contain cycles and branchings. In recent years, NRPs attracted a lot of attention because of their biological activities and pharmacological properties (antibiotic, immunosuppressor, antitumor, etc.). However, few computational resources and tools dedicated to those peptides have been available so far. Norine is focused on NRPs and contains more than 700 entries. The database is freely accessible at http://bioinfo.lifl.fr/norine/. It provides a complete computational tool for systematic study of NRPs in numerous species, and as such, should permit to obtain a better knowledge of these metabolic products and underlying biological mechanisms, and ultimately to contribute to the redesigning of natural products in order to obtain new bioactive compounds for drug discovery.

Show MeSH