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Table of contents

  1. General search
  2. Structure search
  3. Editor
  4. Monomers
  5. Additional information

Structure search Help

Monomeric structure description

In Norine, we use monomeric structures to represent the nonribosomal peptides. These structures are graphs with nodes labelled by monomers. We adopt a convention to write those graphs as formatted strings. We use 3 letter codes for the classical amino acids and add the additional groups for their derivatives such as OH-Asp (Hydroxyaspartic acid) for Asp (Aspartic Acid).
We also design short names for the other compounds. The complete monomer list can be consulted here.

You can search for a structural pattern in all peptides of Norine. The pattern must be specified by a monomeric structure. In addition to the usual graph representations, a structural pattern may have nodes labelled by several alternative monomers. These can be specified by

For exemple, the monomeric structure for vancomycin is : Asn,bOH-Cl-Tyr,NMe-Leu,Hpg,D-Glc,Van,bOH-Cl-Tyr,Dhpg,Hpg @1,3 @0,2,3 @1 @1,0,4,6,8 @3,5 @4 @3,7,8 @6,8 @3,7,6

0 1 2 3 4 5 6 7 8
Asn bOH-Cl-Tyr NMe-Leu Hpg D-Glc Van bOH-Cl-Tyr Dhpg Hpg
@1,3 @0,2,3 @1 @1,0,4,6,8 @3,5 @4 @3,7,8 @6,8 @3,7,6
vancomycin graph exemple

Such graphs can be either obtained from Norine peptide description pages (by copy-paste the "graph representation" lines), or drawn using the dedicated structure editor (consult its help page).

Monomer composition fingerprint search (MCFP)

MCFP is represented as an integer vector, in which each element represents the presence (number of occurrences) or absence ("0" value) of a specific monomer. The process of generating the MCFP for each peptide starts by extracting the monomer compositions from Norine and then filling the corresponding positions in the MCFP vector. A second vector is added from the structure of the peptide, each value is the number of nomoner for a degree value (number of link).

We use Tanimoto-based similarity search system (TAN). This system is based on the Tanimoto coefficient that is a well established method in similarity-based virtual screening and was therefore used as reference. In particular, the continuous form of the Tanimoto coefficient was used. If Ai and Bi represent the ith monomer occurrence and Adegj and Bdegj represents the number of monomer of degree j in the peptides A and B, respectively, then the similarity score SA,B between peptides A and B was calculated by the following equation.

The TAN coefficient varies between 0 (totally different monomer compositions) and 1 (identical monomer compositions). For more information, please consult this article "A new fingerprint to predict nonribosomal peptides activity" (Journal of Computer-Aided Molecular Design, 2012, Vol 26(10), pp 1187-1194, A. Abdo,S. Caboche, V. Leclere, P. Jacques, M. Pupin ).

Structural pattern search

A pattern **occurs** in a peptide graph if it **occurs** as a subgraph, such that each node of the pattern labelled by a monomer is associated to a node of the peptide labelled by the same monomer, and a node labelled by alternative monomers is associated to one of them.

For example, consider the following set of peptide structures :
  1. Ala, Val, His, Pro-Thz, D-Leu @1 @0,2 @1,3 @2,4 @3
  2. Ala, Val, Gly, Pro-Thz, D-Leu @1 @0,2 @1,3 @2,4 @3
  3. Glu, Val, His, Pro-Thz, D-Leu @1,4 @0,2 @1,3 @2,4 @0,3
  4. Ala, Val, His, Pro-Thz, D-Leu @1,2 @0,2 @0,1,3 @2,4 @3
  5. Val, His, Pro-Thz, D-Leu, Ala @1,4 @0,2 @1,3 @2,4 @0,3

Similarity search

Similarity search allows the user to search for peptides which have a similar monomeric structure than the query structure. For each peptide of the Norine database, a distance between the query structure and the query is calculated. The distance ranges from 0, identical strucutures to 1, totally different structures.
The proposed clustering levels are the one presented in the monomers list. No clustering means that only monomers are considered, clustering 1 stands for the inner level of clustering, for example Ala* and clustering 2 for the outer level, for example Ala+Gly.