Structural search

Content:

Introduction

Rhea allow you to perform structural search, substructure or similarity, against ChEBI compounds that are reaction participants.

The facility uses the IDSM Sachem chemical cartridge for fingerprint-guided substructure and similarity searches.

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Import a structure

Ketcher is a web-based chemical structure editor that allow you to draw or import your query structure using SMILES or 2D coordinates (MDL Molfile).

Rhea provides a shortcut to import SMILES. Paste or write a SMILES string in the dedicated text box and click Show button.

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You can also import a structure from the Ketcher interface. Click the Open icon then paste a SMILES or an MDL molfile (Input option). You can also upload a SMILES file or an MDL molfile (File option).

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Substructure search

To retrieve chemical compounds that contain your query structure, you just have to click the Search structure button.

If you want to perform an exact search, select Require exact match option.

Parameters for substructure search (see Sachem documentation for details):

Sachem parameterParameter value
sachem:searchModesachem:substructureSearch
sachem:queryFormatsachem:SMILES
sachem:chargeModesachem:ignoreCharges
sachem:aromaticityModesachem:aromaticityDetect
sachem:isotopeModesachem:ignoreIsotopes (default)
sachem:stereoModesachem:ignoreStereo (default)
sachem:tautomerModesachem:ignoreTautomers (default)

Similarity search

To retrieve chemical compounds that are similar to your query structure, select Similarity search option then click the Search structure button.

Parameters for similarity search (see Sachem documentation for details):

Sachem parameterParameter value
sachem:searchModesachem:similaritySearch
sachem:cutoffuser defined - default 0.8
sachem:similarityRadiususer defined - default 1
sachem:aromaticityModesachem:aromaticityDetect
sachem:tautomerModesachem:ignoreTautomers (default)

Structural search result

The application returns the set of ChEBI compounds that matches your query structure and are participants in Rhea reactions. You can export the resulting set of compounds (full or user-selection) by clicking on the Download button.

In the following example, we use the 2D structure of pyruvic acid (fully protonated form) as query. By using the default parameters, we are able to retrieve pyruvate (CHEBI:15361), the charged forms used in Rhea, as well as other charged molecules (see details in ChEBI major species at pH 7.3)

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