ChEMBL

About

The ChEMBL Database:

Quote

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

• ChEMBL Website
• ChEMBL Web Search
• ChEMBL Downloads

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About this App

Simmate's chembl app helps to download The ChEMBL Database data & load it into the Simmate database.

Module	CLI	Workflows	Data
simmate.apps.chembl

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Installation

1. Add chembl to the list of installed Simmate apps with:

   simmate config add chembl
   

2. Ensure everything is configured correctly:

   simmate config test chembl
   

3. Add new tables to your database:

   simmate database update
   

4. Download all ChEMBL datasets:

   simmate database download chembl
   

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Datasets

Dataset	Disk Space	Rows (#)	SQL Table	Python Class
Molecules	---	---	chembl__molecules	ChemblMolecule
Source Documents	---	---	chembl__documents	ChemblDocument
Molecules	---	---	chembl__assay_results	ChemblAssayResult

Tip

Read through our database guide to learn how to work with these datasets

Example

python

from simmate.database import connect
from simmate.apps.chembl.models import (
    ChemblMolecule,
    ChemblDocument,
    ChemblAssayResult,
)

mol_sample_data = ChemblMolecule.objects.to_dataframe(limit=5_000)
doc_sample_data = ChemblDocument.objects.to_dataframe(limit=5_000)
assay_sample_data = ChemblAssayResult.objects.to_dataframe(limit=5_000)

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