Best for
- Drug discovery and computational chemistry researchers
- Bioinformatics teams needing ChEMBL data through AI assistants
- Developers comfortable with Node.js or Docker
C
ChEMBL MCP Server
Community
Unofficial MCP server providing advanced access to the ChEMBL chemical database
GitHub source repository ↗
75FMRS · B
This server brings the ChEMBL chemical database into the MCP ecosystem with 27 tools and resource templates spanning compounds, targets, activities, drugs, and property analysis—well suited to drug discovery research. As an unofficial project, watch for licensing ambiguity, documentation inconsistencies, and dependence on the ChEMBL API; validate on a small scale before research use.
An unofficial MCP server by Augmented Nature that wraps the ChEMBL REST API with 27 specialized tools covering compound retrieval, target analysis, bioactivity data, drug development information, and chemical property analysis, plus URI-template resource access to ChEMBL data. It communicates over stdio, requires Node.js v16+, and supports Docker deployment. Note: the README is inconsistent about tool count (22 in the intro, 27 in the changelog).
Tools
search_compounds
Search the ChEMBL database by compound name, synonym, or identifier
get_compound_info
Get detailed compound information by ChEMBL ID
search_by_inchi
Find compounds by InChI key or InChI string
get_compound_structure
Retrieve chemical structures in SMILES, InChI, MOL, SDF formats
search_similar_compounds
Find chemically similar compounds using Tanimoto similarity
search_targets
Search for biological targets by name or type
get_target_info
Get detailed target information by ChEMBL target ID
get_target_compounds
Get compounds tested against specific targets
search_by_uniprot
Find ChEMBL targets by UniProt accession
get_target_pathways
Get biological pathways associated with targets
search_activities
Search bioactivity measurements and assay results
get_assay_info
Get detailed assay information by ChEMBL assay ID
search_by_activity_type
Find bioactivity data by activity type and value range
get_dose_response
Get dose-response data and activity profiles
compare_activities
Compare bioactivity data across multiple compounds
search_drugs
Search for approved drugs and clinical candidates
get_drug_info
Get drug development status and clinical trial information
search_drug_indications
Search for therapeutic indications and disease areas
get_mechanism_of_action
Get mechanism of action and target interaction data
analyze_admet_properties
Analyze ADMET (absorption, distribution, metabolism, excretion, toxicity) properties
calculate_descriptors
Calculate molecular descriptors and physicochemical properties
predict_solubility
Predict aqueous solubility and permeability properties
assess_drug_likeness
Assess drug-likeness using Lipinski Rule of Five
substructure_search
Find compounds containing specific substructures
batch_compound_lookup
Process multiple ChEMBL IDs efficiently (1-50)
get_external_references
Get links to external databases (PubChem, DrugBank, PDB, etc.)
advanced_search
Complex queries with multiple chemical and biological filters
Setup
- Clone the repository; 2. Run npm install (requires Node.js v16+); 3. Run npm run build; 4. Add {"mcpServers":{"chembl":{"command":"node","args":["/path/to/chembl-server/build/index.js"]}}} to your MCP client config; 5. Alternatively use Docker: docker build -t chembl-mcp-server . then docker run -i chembl-mcp-server.
claude_desktop_config.json
{"mcpServers":{"chembl":{"command":"node","args":["/path/to/chembl-server/build/index.js"],"env":{}}}}
Fit and risk
Not for
- Production settings requiring official ChEMBL support (this is unofficial)
- Users without a Node.js or Docker environment
- General database tasks unrelated to ChEMBL
Required permissions
- Outbound network access to https://www.ebi.ac.uk/chembl/api/data
- Read-only access to public API data; no authentication credentials required
Risks and side effects
- Unofficial project with license marked NOASSERTION (README claims MIT); verify licensing yourself
- Data accuracy depends on the ChEMBL REST API and the server's parsing may contain defects
- 30-second request timeouts may constrain large batch queries
- README inconsistency on tool count (22 vs 27) raises documentation reliability concerns
Troubleshooting
- Confirm Node.js v16+ is installed and npm run build has completed
- Check network connectivity and firewall rules for ebi.ac.uk
- Verify ChEMBL ID format (e.g., CHEMBL25) is correct
- Reduce limit or batch size if requests time out on large queries
- Inspect MCP client logs for specific error messages
Use cases
Query compounds and their structures/properties by name or ChEMBL ID
Target analysis and retrieval of target-tested compounds
Searching and comparing bioactivity data such as IC50/Ki
Looking up approved drugs, indications, and mechanisms of action
Property analysis including ADMET, molecular descriptors, and drug-likeness
Similarity and substructure searches plus batch ID lookups
Supported clients
Claude DesktopPartial support