Norine

News

March 2021: New release for Norine!

• New tool developed by Ammar Abdo for activity prediction of NRPs from their graph (Activity Prediction)

  Monomer structure fingerprints: an extension of the monomer composition version for peptide databases. Ammar Abdo, Eissa Ghaleb, Naser K. A. Alajmi, Maude Pupin
  Journal of Computer-Aided Molecular Design volume 34, pages 1147-1156 (2020)
  https://link.springer.com/article/10.1007/s10822-020-00336-8

  The web interface has been developped by Clementine Campart
• It is now possible to remove NRPs or set NRPs status as non-NRP (Norine validators only) and to see list of deprecated NRPs. Deprecated NRPs don't appear in structure or annotations search results.
• Bugs fix

Jul. 2020: New release

• New tool developed by Emma Ricart from the SIB (Swiss Institute of Bioinformatics): a tool for the analysis of MS/MS from peptidic natural products (NRPro)
• Update of the pipeline that extract and filter NRPs from external resources
• Adding of missing StreptomeDB links
• Bugs fix

Dec. 2019: Norine release

• Each Norine NRP has been attributed a DOI (Digital Object Identifier):
  To cite a specific peptide, you can now also use its DOI, composed of the 10.26097 prefix and the Norine ID, e.g. https://doi.org/10.26097/nor00342 for the peptide #NOR00342
• Using the rBAN tool to display image of the atomic structure with monomers annotations by infering SMILES, on result page (example)
• Updating Norine licensing and terms of use, see here for more information

Sept. 2019: Major update of the Norine database!

• About 540 new NRPs have been added to the database, automatically extracted and filtered from external resources (MIBiG, BIRD and StreptomeDB)
• These new NRPs are tagged with the 'unreviewed' status
• It is now possible to search peptides according to their origin, i.e. the resource from which it comes from

April 2019: New release for Norine

•   software integration: Run rBAN directly from peptide result page to infer monomeric structure from SMILES
• Database refactoring to improve the handling of peptides' references and journals
• Search for peptides containing some links to external databases (PubChem, PDB...)
• Minor bugs fix

Dec. 2018: Norine database updated!

• About 500 peptides SMILES added or updated after curation process. Thanks to Emma Ricart from SIB, Swiss Institute of Bioinformatics, for her contribution!
• Displaying contributors (creation or modification), on both peptides and monomers page, and all entry history

11/2018: New features for Norine

• Norine contributors are now visible in Contributors tab!
  Access contributions (submitted peptides and modification proposals) for each contributor.
• Displaying more information on recently added or modified peptides (submission date, validator, peptide comment, modifications...)

09/2018: Norine database updated: new SMILES.

• Adding new SMILES to peptides: SMILES is now specified for more than 500 peptides (Thanks to Emma Ricart from SIB, Swiss Institute of Bioinformatics, for her contribution).

07/2018: Norine released!

• Adding missing molecular formulas: now formula is specified for more than 95% of Norine peptides (thanks to Mickael Chevalier from ICV, Institut Charles Viollette for his contribution)
• Run Smiles2Monomers directly from peptide result page to infer monomeric structure from SMILES
• Updating Smiles2Monomers lib. to handle wrong SMILES
• Bug corrections

03/2018: Norine released!

• Monoisotopic mass is now automatically calculated from molecular formula for both monomers and peptides (Thanks to Emma Ricart from SIB, Swiss Institute of Bioinformatics, for her help)
• Upgrading Smiles2Monomers lib.
• Bug corrections

10/2017: Norine released!

• New features in annotations search: filter peptides that have a smiles defined
• Taxonomy tree have been updated for producing organisms
• New REST service: get peptides with smiles (see documentation)
• Bug corrections

12/2016: New release of Norine

• New annotations search interface: create dynamic and advanced requests
• Refactoring of norine database structure
• Use now the Smiles2Monomers tool as a web service : see here
• New peptide result page
• MyNorine: enhanced interfaces for defining organisms' taxonomy and monomers' clustering

06/2016: Norine is now referenced on OMICStool

• OMICtools is a workflow for multi-omics data analysis. Norine is referenced in the category : Dataset > Drug discovery > Peptide prediction 

01/2016: New release of MyNorine

• MyNorine now automatically compares the monomeric composition of a new peptide submission, with the composition inferred by Smiles2Monomers, if the SMILES is given.
• Updating the S2M wrapper.
• New publication available
  • Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing. Areski Flissi, Yoann Dufresne, Juraj Michalik, Laurie Tonon, Stéphane Janot, Laurent Noé, Philippe Jacques, Valérie Leclère and Maude Pupin
    Nucl Acids Res 2016, Nov. 2015, doi: 10.1093/nar/gkv1143
• Minor bugs fixed

09/2015: New graphical editor for peptides

• New editor for Norine: the editor allowing to draw monomeric structure/composition of NRPs is now coded in JavaScript.
• New visualisator for peptides in result pages.

08/2015: New features for Norine!

• New features for Norine: additional smiles information for some peptide, and atomic structure image (automatically generated using the Smiles2Monomers tool from smiles) for monomers and peptides
• MyNorine: the tool allows now to also submit proposal of modifications for NRPs entries; theses proposals will be manually checked and validated by the Norine team
• New peptides added to the database, and some entries have been corrected.

01/2015: New release of Norine!

• Refactoring of Norine code for optimization purpose
• New features: save XML/Json data for each peptide, import peptide template to MyNorine
• MyNorine : a new interface dedicated to the submission of new non-ribosomal petides to Norine database:
  • More information
• Norine REST Services: useful REST services to access the Norine database:
  • See documentation here
• Bugs fixed

07/2013: Norine is still alive

• Norine contains now 1164 peptides and others will come this automn
• Some entries have been corrected
• Norine code has moved under Model-view-controller architecture, but the functionalities are still effective
• A new structure search form is available with improved features (see help for more details)
• Structure search can be done by monomer fingerprint, as presented in our article :
  • A new fingerprint to predict nonribosomal peptides activity.
    Abdo A, Caboche S, Leclere V, Jacques P, Pupin M.
    J Comput Aided Mol Des. 2012 Oct;26(10):1187-94, doi: 10.1007/s10822-012-9608-4
• Minor bugs fixed

04/2010: Norine features are upgraded:

• Norine contains now 1122 peptides
• A new version of the structure editor is available
• Monomers and peptides are presented grouped to help their search
• You can now have the list of peptides produced by an organism
• Minor bugs were corrected

06/22/2009: Norine gets enriched by new features:

• You can download Norine data as XML or text files
• Similarity search is now available here

03/10/2009: New release of Norine:

• The new release of Norine contains 1071 peptides
• Fatty acids are encoded and all fatty acid variants of a peptide are available
• Structural pattern matching allows a search for peptides containing the pattern substructure with a given minimal number of monomers. for more information see:
  • Structural pattern matching of nonribosomal peptides,
    Segolene Caboche, Maude Pupin, Valerie Leclere, Philippe Jacques and Gregory Kucherov,
    BMC Structural Biology 2009, 9:15, doi: 10.1186/1472-6807-9-15
• A more detailled description of each monomer is available (e.g. molecular weight, SMILES, molecular formula)

08/08/2008: Norine gets enriched by new features:

• You can submit a new peptide or modifications
• For each peptide, you can add comments
• Changes in search forms

Norine has been presented for the first time to the JOBIM 06 conference (poster and flash presentation).

In June 2007, a Norine poster has been presented to the 7th congress of the French Society for Microbiology in Nantes, where it has been awarded best poster over than more 300 posters presented.

Last entries (0)

What are nonribosomal peptides

Bacteria or fungi feature peptides that are synthesized through a ribosome independent pathway rather than through the classical pathway from the DNA transcription to the translation of mRNA into peptides on the ribosome. This alternative pathway is called NonRibosomal Peptide Synthesis. It is performed by a huge protein complex called a NonRibosomal Peptide Synthetase (NRPS). This is a modularly organized multi-enzyme complex that bears template and biosynthetic machinery at the same time. The molecules synthesized by NRPS are short (two to about fifty monomers), include a high proportion of nonproteogenic amino acids and often contain amino acids connected by bonds other than peptide or disulfide bonds. The diversity of amino acids incorporated in NRPS peptides is large and it is why we prefer to speak of monomers rather than amino acids. Therefore the primary structure of nonribosomal peptides is not always linear. They can form cycles (partial or not) and branchings.
Nonribosomal peptides have a broad range of biological activities and pharmacological properties, for example immunomodulating, iron chelating or antimicrobial activities. The latter is illustrated by the famous penicillin which is synthesized from ACV-tripeptide precursor produced by NRPS pathway.
For more details about the monomers stored in Norine, you can read our paper :
Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity. Caboche S, Leclere V, Pupin M, Kucherov G, Jacques P.
J Bacteriol. 2010 Oct;192(19):5143-50, doi: 10.1128/JB.00315-10

Latest news:

March 2021: New release for Norine!

• New tool developed by Ammar Abdo for activity prediction of NRPs from their graph (Activity Prediction)

  Monomer structure fingerprints: an extension of the monomer composition version for peptide databases. Ammar Abdo, Eissa Ghaleb, Naser K. A. Alajmi, Maude Pupin
  Journal of Computer-Aided Molecular Design volume 34, pages 1147-1156 (2020)
  https://link.springer.com/article/10.1007/s10822-020-00336-8

  The web interface has been developped by Clementine Campart
• It is now possible to remove NRPs or set NRPs status as non-NRP (Norine validators only) and to see list of deprecated NRPs. Deprecated NRPs don't appear in structure or annotations search results.
• Bugs fix

Jul. 2020: New release

• New tool developed by Emma Ricart from the SIB (Swiss Institute of Bioinformatics): a tool for the analysis of MS/MS from peptidic natural products (NRPro)
• Update of the pipeline that extract and filter NRPs from external resources
• Adding of missing StreptomeDB links
• Bugs fix

Dec. 2019: Norine release

• Each Norine NRP has been attributed a DOI (Digital Object Identifier):
  To cite a specific peptide, you can now also use its DOI, composed of the 10.26097 prefix and the Norine ID, e.g. https://doi.org/10.26097/nor00342 for the peptide #NOR00342
• Using the rBAN tool to display image of the atomic structure with monomers annotations by infering SMILES, on result page (example)
• Updating Norine licensing and terms of use, see here for more information

Sept. 2019: Major update of the Norine database!

• About 540 new NRPs have been added to the database, automatically extracted and filtered from external resources (MIBiG, BIRD and StreptomeDB)
• These new NRPs are tagged with the 'unreviewed' status
• It is now possible to search peptides according to their origin, i.e. the resource from which it comes from

SiteMap

Contact informations

This project results from a tight collaboration between the Bonsai bioinformatics research group of CRIStAL (Centre de Recherche en Informatique, Signal et Automatique de Lille, ex-LIFL (Laboratoire d'Informatique Fondamentale de Lille) and Inria (Institut National de Recherche en Informatique et en Automatique) and the NRPS team from the ProBioGem laboratory (Laboratoire des Procédés Biologiques Génie Enzymatique et Microbien).
The Norine Team is composed of contributors of these two labs.

All inquiries should be sent to Norine (norine_at_univ-lille.fr).

This project is supported by bilille and the French Institute of Bioinformatics (IFB).

Norine database contributors

Norine is mainly maintained by the Norine team composed of members of the CRIStAL lab. (CNRS, the French National Scientific Research Center, and University of Lille, France) and the ProbioGem team of the Charles Viollette Institute (ICV), France.

People who also contributed to the Norine database by submitting new NRPs or modification proposals: