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chembl-database

Query ChEMBL for molecules, targets, and bioactivity data.

18|1|Updated Dec 27, 2025
Search Tags:#bioactivity#drug-discovery#chembl#similarity-search#substructure-search#molecule-queries#target-queries
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill chembl-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: chembl-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/chembl-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill chembl-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Retrieve and organize molecular, target, and bioactivity data from the ChEMBL database to support medicinal chemistry research and lead optimization tasks.

Core Features & Use Cases

  • Molecule Queries: Retrieve compounds by ChEMBL ID, name, or property filters.
  • Target Queries: Access biological targets and related metadata.
  • Bioactivity Data: Fetch IC50, Ki, EC50 and other activity measurements for compounds and targets.
  • Structure-Based Searches: Perform similarity and substructure searches using SMILES strings.
  • Drug Information: Retrieve drug data, mechanisms of action, and indications.

Quick Start

Run the included example_queries.py to see practical ChEMBL queries in action.

Frequently Asked Questions about chembl-database

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

FAQPage Schema
How do I retrieve IC50 and Ki bioactivity data from ChEMBL for drug discovery?▼

Retrieve IC50, Ki, and EC50 bioactivity data from ChEMBL by applying filters to compound and target queries. The tool fetches activity measurements directly via the chembl_webresource_client to support medicinal chemistry research and SAR analysis.

Can I perform a substructure search in ChEMBL using a SMILES string?▼

Yes, you can perform substructure and similarity searches in ChEMBL using SMILES strings. The tool passes the SMILES input to the chembl_webresource_client to find matching molecules for structure-based drug discovery workflows.

What's the best way to query ChEMBL molecules by ChEMBL ID or name?▼

Query ChEMBL molecules by ChEMBL ID, name, or property filters using the chembl_webresource_client. The tool retrieves matching compound records and organizes the molecular data with pandas for medicinal chemistry research.

Does the ChEMBL database tool require pandas to export bioactivity data?▼

Yes, the ChEMBL database tool requires pandas as a dependency to organize and export molecular, target, and bioactivity data. It uses chembl_webresource_client to fetch records and pandas to structure the query outputs.

How do I access biological target metadata for target exploration in ChEMBL?▼

Access biological target metadata by running target queries against the ChEMBL database. The tool retrieves related target information via the chembl_webresource_client to support target exploration and drug discovery workflows.

Can I retrieve drug mechanisms of action and indications from ChEMBL data?▼

Yes, you can retrieve drug mechanisms of action and indications from ChEMBL data. The tool queries the chembl_webresource_client to fetch drug information, supporting lead optimization and drug discovery research tasks.

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