Chemical substructure search

How to find molecules with a chemical substructure?

Enter a library of SMILES and a SMARTS query describing the atom and bond pattern to find. Chemical substructure search returns matching compounds, match counts and atom indices. Download the matches as SMILES or SDF, or inspect which compounds contain a ring or functional group.

1. Paste the compounds to search, one SMILES per line.
2. Enter the pattern in SMARTS query. The default finds a benzene ring.
3. Run the search.
4. Review match counts and download the matching structures.

Worked example

Input SMILES:

Cc1ccccc1 toluene
CCO ethanol

The default SMARTS c1ccccc1 finds the benzene ring in toluene, while ethanol does not match:

Name	SMILES	Match count	Atom matches
toluene	Cc1ccccc1	1	[[1, 2, 3, 4, 5, 6]]

Input

Put the SMILES first, for example CCO ethanol, rather than a header row or name-first column. Blank lines are ignored. Unnamed molecules receive generated identifiers. Invalid SMILES fail the job instead of being silently dropped.

Settings

Results

Downloads are available from Files. The exported records retain returned row order.

SMARTS patterns versus SMILES molecules

SMILES describes a molecule. SMARTS describes a query pattern with atom alternatives, aromaticity, charge, bond types and logical conditions. This tool reads the library as SMILES and the query as SMARTS.

Encode the distinctions needed for the search. A broad carbonyl-and-oxygen pattern can match acids or esters; add atom and bond conditions when those differences matter.

Atom mappings use zero-based RDKit indices in the parsed molecule, not PDB serial numbers. Each mapping lists target atoms in query-atom order. Symmetry can produce equivalent mappings; Unique matches determines whether they are retained. Each matched compound appears once in the table.

Substructure search or chemical similarity search?

Use molecular similarity search for approximate resemblance even when an exact motif is absent. Use Butina clustering to group the whole library rather than filter it.

FAQ

Does this search a public chemical database?

It searches only the compounds you submit. It does not query an external database.

What happens if no compounds match?

The job completes with an empty table and empty molecule exports. No match is a valid search result.

Does substructure search require matching stereochemistry?

Only when Match stereochemistry is on and the SMARTS specifies it. Otherwise stereochemical constraints are ignored.