ChEMBL MCP Server

A Model Context Protocol (MCP) server exposing ChEMBL's public bioactivity database as tools usable by Claude and ChatGPT.

Tools

Tool	Purpose
search_compounds	Search ChEMBL by compound name/synonym
get_compound_bioactivity	Get bioactivity records for a ChEMBL ID
get_target_compounds	Get active compounds against a target
get_admet_properties	Get computed physicochemical/ADMET properties

Run locally

pip install -r requirements.txt
python3 server.py

Server starts on 0.0.0.0:8000, MCP endpoint at /mcp (streamable HTTP).

IT deployment checklist

1. Host: Deploy on a small VM/container (Railway, Render, AWS ECS, or internal cloud). 1 vCPU / 512MB RAM is sufficient — server only proxies to ChEMBL's public REST API, no local DB.
2. Public HTTPS: Expose at a subdomain, e.g. chembl-mcp.excelra.com, with TLS (Let's Encrypt or managed cert).
3. Reverse proxy: nginx/Caddy → forward to localhost:8000.
4. Env/firewall: outbound HTTPS to www.ebi.ac.uk must be allowed.
5. No auth required for MVP (ChEMBL data is public). Add an API key header check in server.py later if you want to gate access.

Connecting to Claude / ChatGPT

• Claude.ai / Claude Desktop: Settings → Connectors → Add custom connector → enter https://chembl-mcp.excelra.com/mcp
• ChatGPT: Settings → Connectors → Advanced → Developer Mode → Add remote MCP server → same URL

Next steps / extensions

• Add get_drug_indications, get_similar_compounds (structure similarity)
• Cache common ChEMBL responses (Redis) to reduce latency/rate-limit risk
• Swap public REST API for a local ChEMBL Postgres mirror if query volume grows (faster, no rate limits)
• This same scaffold pattern (FastMCP + REST wrapper) is directly reusable for a future GOSTAR MCP server