db-substructure-similarity-search.md

Database substructure and similarity search

Efficient substructure and similarity searching in a database containing information about molecules is a key requirement for any chemical information management system. This is typically done by installing a so-called chemical cartridge on top of a database server. The cartridge extends server's functionality with the molecule-specific operations, which are made efficient by using chemically-aware indexes, which are often based on molecular fingerprints. Typically, these operations are functions that can be used as part of the SQL query.

Chemical cartridge

Datagrok provides mechanisms for the automated translation of queries into SQL statements for several commonly used chemical cartridges. We support the following ones:

1. RDKit Postgres cartridge
2. JChem cartridge (todo)

Here are some of the examples of substructure and similarity searches against ChEMBL using RDKit cartridge. These examples are regular Grok queries, meaning that they can be easily created, managed, and used from within the platform.

Substructure search:

--name: @pattern substructure search
--connection: chembl
--input: string pattern {semType: Substructure}
--input: int maxRows = 1000
 select molregno,m as smiles from rdk.mols where m@>@pattern
 limit @maxRows

Similarity search:

--name: @pattern similarity search
--connection: chembl
--input: string pattern {semType: Substructure}
--input: int maxRows = 1000
select fps.molregno, cs.canonical_smiles as smiles
from rdk.fps fps
join compound_structures cs on cs.molregno = fps.molregno
where mfp2%morganbv_fp(@pattern)
limit @maxRows

See also:

• Queries
• Functions