F
licenseB
qualityD
maintenanceA comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.
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ChEMBL MCP Server
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@ChEMBL MCP ServerFind active compounds against EGFR"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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 ChEMBL by compound name/synonym |
| Get bioactivity records for a ChEMBL ID |
| Get active compounds against a target |
| Get computed physicochemical/ADMET properties |
Related MCP server: ChEMBL-MCP-Server
Run locally
pip install -r requirements.txt
python3 server.pyServer starts on 0.0.0.0:8000, MCP endpoint at /mcp (streamable HTTP).
IT deployment checklist
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.
Public HTTPS: Expose at a subdomain, e.g.
chembl-mcp.excelra.com, with TLS (Let's Encrypt or managed cert).Reverse proxy: nginx/Caddy → forward to
localhost:8000.Env/firewall: outbound HTTPS to
www.ebi.ac.ukmust be allowed.No auth required for MVP (ChEMBL data is public). Add an API key header check in
server.pylater 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/mcpChatGPT: 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
This server cannot be deployed
Maintenance
ActivityInactive
ResponsivenessNo issues
Related MCP Connectors
ChEMBL MCP — drug discovery database (EBI).
AI-powered bioprotocol optimization — generate, search, and manage lab protocols via MCP
MCP server unifying ERPs, CRMs, APIs and knowledge base for Claude, ChatGPT and Gemini.
Auditable MCP server for PubMed, Europe PMC, ClinicalTrials.gov, and bioRxiv/medRxiv queries
Related MCP Servers
- FlicenseNot gradedqualityDmaintenanceA FastMCP wrapper server that provides API access to the ChEMBL database, enabling users to query drug discovery data such as activities, assays, targets, and molecules.2-
- AlicenseNot gradedqualityCmaintenanceUnified MCP server providing AI-agent-ready access to AlphaFold, PubMed, ChEMBL, Ensembl, and 37+ scientific databases.MIT
- AlicenseAqualityAmaintenanceAn MCP server that gives AI assistants access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).2913MIT