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db-chembl

Query ChEMBL for bioactive molecules and drug discovery data via chembl_webresource_client.

Updated Mar 13, 2026
Search Tags:#drug discovery#bioactivity#target identification#cheminformatics#chembl#molecule search
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-chembl
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-chembl
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-chembl
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-chembl

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the ChEMBL database, enabling researchers to query vast amounts of bioactive molecule and drug discovery data, accelerating research and development.

Core Features & Use Cases

  • Molecule & Target Queries: Search for compounds by ID, name, or properties; retrieve information on biological targets.
  • Bioactivity Data: Find inhibitors, agonists, and other bioactive molecules with specific activity thresholds (e.g., IC50, Ki).
  • Structure-Based Searches: Perform similarity and substructure searches to identify related compounds.
  • Drug Information: Retrieve details on approved drugs, their mechanisms of action, and indications.
  • Use Case: A medicinal chemist can use this Skill to find all compounds similar to a lead molecule that inhibit a specific protein target with an IC50 below 100 nM.

Quick Start

Use the db-chembl skill to find all compounds with an IC50 less than 10 nM for the target CHEMBL203.

Frequently Asked Questions about db-chembl

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

FAQPage Schema
How do I query ChEMBL for bioactive molecules with specific IC50 thresholds?▼

To query ChEMBL for bioactive molecules, use this Skill to filter compounds by target and specific IC50 thresholds, retrieving results directly as pandas DataFrames for drug discovery analysis.

Can I perform structure-based similarity searches for drug discovery compounds?▼

Yes, you can perform structure-based similarity and substructure searches through the ChEMBL database to identify related compounds and retrieve their bioactivity data for medicinal chemistry research.

What is the best way to retrieve approved drug information and mechanisms of action from ChEMBL?▼

The best way to retrieve approved drug information is by querying the ChEMBL database for drug indications and mechanisms of action, exporting the retrieved molecular and target data directly to pandas DataFrames.

Does this ChEMBL search method require pandas to export bioactivity data?▼

Yes, pandas is a required dependency to format and export retrieved ChEMBL bioactivity data, molecule properties, and target information into structured DataFrames for cheminformatics analysis.

How do I find all compounds similar to a lead molecule that inhibit a specific protein target?▼

You can find inhibiting compounds by combining structure-based similarity searches with advanced filtering for specific protein targets and activity thresholds, leveraging the chembl_webresource_client for data retrieval.

What are the limitations of using chembl_webresource_client for molecule searches?▼

Limitations include dependency on the external ChEMBL web service for availability and speed, meaning complex cheminformatics queries involving extensive substructure searches or large dataset retrieval to pandas may experience network latency constraints.

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