====== Substructure search ======

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Substructure search identifies molecules that contains a specific fragment (substructure).

===== When to use =====
 

Substructure searching is frequently applied for hit exploration. Unlike [[similaritysearch|similarity searching]], it outputs only those molecules containing the whole query molecule. It can therefore retrieve close analogs of a particular scaffold (e.g. [[http://en.wikipedia.org/wiki/High-throughput_screening|HTS]] hit or reference ligand), which can be used to build an initial [[http://en.wikipedia.org/wiki/Structure-activity_relationship|SAR]] (structure-activity relationship).

===== How to use =====


If your first query does not yield enough hits, it is recommended to fine-tune your substructure search and use a more general query. If you get too many hits, you can block certain substitution positions by adding explicit hydrogens (see example in Figure). Multicomponent queries are currently not supported.

==== Option ====


It is possible to set whether the substructure search should be performed on the specific tautomer (and protonation state) specified in the input, or the search is tautomer (and protonation state) independent (**“Tautomer independent”** box).

Queries can be drawn by the [[sketcher|molecule sketcher]], which can be hidden and reopened by clicking on the “Hide/Show sketcher” link. Queries can be also defined by entering mcule IDs, [[http://www.inchi-trust.org/inchi|InChI]] or [[http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html|SMILES]] strings into the input field. 2D representations can be generated by clicking on the “Generate 2D” button. Note: If the “Generate 2D” button was clicked, the search will be performed on the generated 2D representation (2D SDF exported from the [[sketcher|sketcher]]). If, however, the “Generate 2D” button was not clicked, the search will be directly performed on the mcule ID, [[http://www.inchi-trust.org/inchi|InChI]] or [[http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html|SMILES]] strings coming from the input field. The results might be slightly different in these two cases.

===== Results =====

Molecules satisfying search criteria