Norine

Table of contents

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

General search Help

Common features

• When several fields of the general search page are completed (such as name AND activity), the entries returned match all of them.
• The search is not case-sensitive. It does not matter whether you use capital or lower case letters.
• Singular Term Finds Plurals. Using a singular word form will retrieve both singular and plural forms of this word.
• One term Finds sentence. Using one term will retrieve the whole sentence.

Basic search

First you can search by the Norine identifier that starts with the 'NOR' prefix followed by 5 digits. You can also search by general or specific peptide name. A specific name represents the exact name of an NRPS peptide (example: cyclosporin A). If the peptide is present in the database, you will obtain only one entry. A general name represents a generic name for the NRPS peptide (example: cyclosporin). This search can give several peptide variants belonging to the same group.
You can use the following Boolean operators in your query, by selecting from the drop-down list in the search form:

• AND: only peptide names matching both terms are found.
• OR: peptide names matching at least one of the terms are found.
• AND NOT: peptide names matching the first term and not matching the second one are found.

You can also search by peptide activity or by structure type. The activity field corresponds to the peptide biological activity, such as antimicrobial or siderophore. The structure type specifies the peptide structure such as cyclic or linear.

Peptides can also be searched by their molecular weight. To do this, the user has to specify an interval.

You can search for peptides containing exactly, less than or more than a given number of monomers.

You can also obtain all the peptides that contain a specific monomer. For this, enter the monomer code. For example, querying Thr (for threonine) will output the list of peptides having threonine in its composition.
You can also obtain all the peptides containing a given monomer and its derivatives. For example, querying Thr gets all the peptides containing not only the threonine amino acid, but also D-treonine, allo-threonine or methyl-threonine amino acids.

Bibliography reference search

This part allows a search for peptides by associated bibliographic references. One can search by author, title, year of publication, journal, or by pmid (PubMed identifier).
You can type in several text box. For example, you can specify an author, and a journal name.
You can use Boolean operators (AND, OR, AND NOT) in your query, as described in Basic search.

Organism search

In this part, the search is done on organims from which the corresponding peptides were extracted. We think that sometimes those are not the producing organisms. The user can specify whatever taxonomic level. For example, querying bacteria will output all the peptides produced by bacteria, and querying bacillus subtilis will output only those extracted from this organism. You can use Boolean operators (AND, OR, AND NOT) in your query as described in Basic search.

Lists

You can obtain the whole list of peptides contained in the database by clicking on the 'Peptides' button.
You can obtain the whole list of organisms included in the database by clicking on the 'Organisms' button.