Structure search

Content:

Introduction

We use the IDSM Sachem chemical cartridge for fingerprint-guided substructure and similarity searches. You can enter a query structure and search reaction participants that contain your structure or are similar to it.

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Import a structure

Use the chemical structure editor Ketcher to draw a structure or import your query structure using SMILES or 2D coordinates (MDL Molfile).

Instructions

  • Option 1:
    Enter a SMILES string in the dedicated text box and click the Show button.

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  • Option 2:
    Use the Ketcher interface: Click the Open icon and enter a SMILES/MDL molfile (Input option) or upload a file with a SMILES/MDL molfile (File option).

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Substructure search

This is the default option. To retrieve chemical compounds that contain your query structure, just click the Search structure button.

If you want to perform an exact search, select the 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
sachem:stereoModesachem:ignoreStereo
sachem:tautomerModesachem:ignoreTautomers

Similarity search

To retrieve chemical compounds that are similar to your query structure, select the 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

Search results

The search returns the set of ChEBI compounds that match your query structure and that are participants in Rhea reactions. You can export these compounds (all or a selection) by clicking the 'Download' button.

In the following example, we search with the 2D structure of pyruvic acid (the fully protonated form). With the default parameters, we retrieve pyruvate (the major microspecies at pH 7.3 that is used in Rhea), as well as other charged molecules.

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