Help/FAQ

In StreptomeDB each metabolite is connected to the producing species of the genus Streptomyces. You can start a search by querying the natural compound or the producing organism.

Compounds

If you know the name of the compound of interest just type in the name or synonym. If the compound is also included in the PubChem database you can also type in the related PubChem-ID (e.g. CID:3033).

Furthermore, there is the possibility to search for compounds ordered alphabetically. To do so, navigate to "Compounds (list)" respectively "compound list".

Sometimes the name is not clearly defined or not known but the structure of the compound. In that case it is possible to draw the structure by using JSDraw. It is not neccessary to match the exact structure, similar structures will also be identified.

It is possible to change search parameters e.g. decrease the tanimoto coefficient to increase the number of similar compounds. Additionally you can decide to search for substructures, e.g. you draw a tricyclic structures to get all tricyclic compounds produced by Streptomyces.

Additionally, it is possible to browse through the database by a set of constraints of physico chemical properties.

The result window provides a table with identified compounds that are related to Streptomcyes species. With a click on the compound name a compound card appears with detailed information.

Organisms

The second search option provides the possibility to search for the names of the source organisms, alphabetically and/or via search term.

The result table shows resulting organisms of Streptomyces and the number of associated compounds. Sub-strains are merged to the main strain. To get the detailed information for the sub-strains click on "show strains". To get information for the compounds produced by this organism, click on the number in the column "Compounds Associated".

Synthesis Pathways

It is possible to search specifically for the pathways in which compounds are synthesized in. You can select "All" or one or more of the main classes of synthesis pathways to receive a list of compounds produced by those pathways. Additionally you can specify terms to narrow your searches. Click on the compound name to get a detailed description of the compound. If PubMed IDs of the describing articles are available, they are shown in the "PMIDs" column. Click on a PubMed ID to see associated abstracts.

Activities

A fourth possibility is to search specifically for activities assigned to the compounds. You can select "All" or one or more of the main classes of activities to receive a list of compounds assigned to those activities. Additionally you can specify terms to narrow your searches. Click on the compound name to get a detailed description of the compound. If PubMed IDs of the describing articles are available, they are shown in the "PMIDs" column. Click on a PubMed ID to see associated abstracts.

Scaffold browser

Scaffolds can be searched through directly. The search table shows all available scaffolds sorted by frequency of occurence, starting in scaffold level 0. After selecting one or more stuructures, you can either decide to browse through the next level of scaffolds containing the previously selected structures, or to show all related compounds.

NMR/MS

StreptomeDB provides thousands of predicted NMR and MS spectra. You can specify multiplicity, chemical shift, and wheather you are looking for 1H or 13C results for any number of signals. The multiplicity can be specified to a certain point(S = singulet; D = doublet; T = triplet; D.T = dublet of a triplet; T.T = triplet of a triplet), any other multiplicity can be found by choosing M(multiplet). You can also search for any number of MS peaks by mass-to-charge ratio (tolerance is 0.2 m/z).

Phylogenetic Tree

The phylogenetic tree is based on 16S rRNA. Strains with a common ancester node within range of 0.07 are clustered by the same background color. Substrains and mutants are summarized: Clicking on the leaf "S. griseus" leads to a list of all compounds produced by Streptomyces griseus itself and all of its mutants and substrains. The host organisms of any search result can be highlighted in the tree by clicking "View the phylogeny tree of the organisms associated with the following compounds" on top of any resultstable.

2D similarity search

Similarity searches in StreptomeDB are conducted within it's PostgreSQL database with the pgchem module using 2D Daylight-like fingerprints or substructure searches. Those fingerprints represent structural features of a molecule. Fingerprints are dichotomous [0,1] (bit) arrays. Rather than encoding concrete structural features like structural keys do, there is no assigned meaning to each bit. Fingerprints are generated from the molecule itself using hash algorithms. There are

  • patterns for each atom,
  • patterns for each atom, nearest neighbors, and respective bonds,
  • patterns for each atom group and bonds for paths of up to two, three, ..., and seven bonds in length.

Subsequently, those patterns are generally encoded in four to five bits and added to the fingerprint. If patterns are substructures of another structure, all bits set in the substructure pattern's fingerprint will be set in the other's fingerprint. Boolean operations on those fingerprints provide an effective way for similarity calculations and substructure searches. Stereochemistry as well as atoms not connected to the "main" molecule are not considered in the kind of search StreptomeDB perfoms.

StreptomeDB uses the tanimoto coefficent for similarity calculations:

tcA,B=NA,B/(NA+NB-NA,B), with

  • NA number of bits set "on" in fingerprint of molecule A
  • NB number of bits set "on" in fingerprint of molecule B
  • NA,B number of bits set "on" in fingerprint of both molecules (A and B).
A tanimoto coefficient of 0.85 (or 85%) is widely accepted to be sufficiently similar for first guesses that biological activities of one molecule might be comparable to another.

FAQs

What is StreptomeDB?

StreptomeDB is a database that stores information of natural compounds produced by bacteria of the genus Streptomyces. These metabolites are very important for the production of natural drugs such as antibiotic, antitumor or immunosuppressant drugs. In addition to the structures of the compounds, we have included information about source organisms, references, biological role, activities, and syntheses-routes (e.g. polyketide synthase (PKS)-derived, non-ribosomal peptides (NRPs)-derived).

Which input formats can be used for structural searches?

By using the icon for structures in the editor, you can transfer files in mol, html, and rxnfile formats. To import a structure paste file contents (text) in the text area and press open.

What does the tanimoto coefficient tell me?

Fingerprints are {0,1}-strings representing structures (i.e. structure features, properties or paths) and can be used to calculate similarity coefficients between structures represented by fingerprints. Several widely accepted coefficients exist - we went for the tanimoto coefficient. Values are between 0 (completely different) to 1 (equal fingerprint). We recommend PMID: 20450209 or similar for further reading.

What is a reasonable cut-off value for the tanimoto coefficient?

For a first try, 0.85 (or 85%) is a widely accepted value. If searches yield too many or too few results (use the "estimate" option on the "change parameters" site) you can slowly adapt the tanimoto until you retrieve an adequate number of similar compounds.

What is shown if I click on a compound name?

If you click on a compound name, StreptomeDB provides information about the compound, such as synonyms, predicted physico chemical properties, related organisms including available genomes, corresponding references, additional information about similar compounds, compound activity, the synthesizing routes, available gene clusters, and scaffolds.

Which browsers can be used?

StreptomeDB has been tested with IE8, FF3.5+, and webkit browsers (Safari, Google Chrome). Although, all modern browsers of any brand should work fine.

How to cite StreptomeDB?

Please, cite accession date, time, and the url "http://StreptomeDB.pharmaceutical-bioinformatics.de"

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