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JosephWoodall
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chembl-database

Query ChEMBL molecules, targets, and bioactivities with Django-style filters.

1|Updated Mar 19, 2026
Search Tags:#bioactivity#cheminformatics#drug-discovery#structure-search#chembl#data-export#molecular-queries
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill chembl-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: chembl-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/chembl-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill chembl-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires chembl_webresource_client, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

ChEMBL provides millions of bioactive compounds, targets, and bioactivity measurements. This Skill enables programmatic access to molecule, target, and activity data for discovery workflows and research automation.

Core Features & Use Cases

  • Molecule queries: retrieve by CHEMBL ID, search by name, and filter by properties.
  • Target queries: fetch target details and search by type or organism.
  • Bioactivity data: access IC50/Ki/EC50 data and pChEMBL normalization.
  • Structure-based searches: perform similarity and substructure queries.
  • Drug information: obtain drug data, mechanisms, and indications.
  • Use in SAR studies and drug-discovery pipelines with reproducible queries.

Quick Start

Query a molecule or target by CHEMBL ID or name to retrieve details and bioactivities with this tool.

Frequently Asked Questions about chembl-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve ChEMBL bioactivity data like IC50 and Ki values programmatically?▼

Retrieve ChEMBL bioactivity data by querying activity endpoints to access IC50, Ki, and EC50 measurements, applying pChEMBL normalization for standardized values across drug discovery workflows.

Can I perform molecular structure searches for similarity and substructure in ChEMBL?▼

Perform molecular structure searches in ChEMBL by executing similarity and substructure queries against molecule endpoints to identify compounds for medicinal chemistry and SAR studies.

What's the best way to export ChEMBL molecule and target query results for analysis?▼

Export ChEMBL molecule and target query results directly into a pandas DataFrame to enable structured data analysis and integration into drug repurposing pipelines.

Does this tool support filtering ChEMBL targets by organism and target type?▼

Filter ChEMBL targets by organism and target type using Django-style filters applied to target endpoints, fetching specific target details for discovery workflows.

Can I query ChEMBL drug mechanisms and indications for drug repurposing workflows?▼

Query ChEMBL drug mechanisms and indications by retrieving drug data through molecule endpoints, supporting drug repurposing workflows and reproducible research automation.

How do I search ChEMBL molecules by name or CHEMBL ID for target discovery?▼

Search ChEMBL molecules by name or CHEMBL ID through molecule query endpoints to retrieve compound details and associated bioactivities for target discovery and SAR studies.

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