ChEMBLSAFE
A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database. This server offers 22 specialized tools enabling AI assistants and MCP clients to perform sophisticated drug discovery research, chemical informatics analysis, and bioactivity investigations directly through ChEMBL's REST API.
Developed by [Augmented Nature](https://augmentednature.ai)
Features
Core Chemical Search & Retrieval (5 tools)
- Compound Search: Search the ChEMBL database by compound name, synonym, or identifier
- Detailed Compound Info: Retrieve comprehensive compound information including structure, properties, and annotations
- InChI-based Search: Find compounds by InChI key or InChI string
- Structure Retrieval: Get chemical structure information in various formats (SMILES, InChI, MOL, SDF)
- Similarity Search: Find chemically similar compounds using Tanimoto similarity
Target Analysis & Drug Discovery (5 tools)
- Target Search: Search for biological targets by name or type
- Detailed Target Info: Retrieve comprehensive target information and annotations
- Target Compounds: Get compounds tested against specific targets
- UniProt Integration: Find ChEMBL targets by UniProt accession numbers
- Target Pathways: Associated biological pathways and mechanisms
Bioactivity & Assay Data (5 tools)
- Activity Search: Search bioactivity measurements and assay results
- Detailed Assay Info: Get comprehensive assay protocols and conditions
- Activity Type Search: Find bioactivity data by specific activity type and value range
- Dose-Response Analysis: Get dose-response data and activity profiles
- Activity Comparison: Compare bioactivity data across multiple compounds or targets
Drug Development & Clinical Data (4 tools)
- Drug Search: Search for approved d
77625e6efd48OBSERVED · 2026-10-07Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add chembl-server -- npx -y [email protected]
{
"mcpServers": {
"chembl-server": {
"command": "npx",
"args": [
"-y",
"[email protected]"
]
}
}
}Exposed tools (27)
27 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
advanced_search | read | Complex queries with multiple chemical and biological filters |
analyze_admet_properties | read | Analyze ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity) |
assess_drug_likeness | read | Assess drug-likeness using Lipinski Rule of Five and other metrics |
batch_compound_lookup | read | Process multiple ChEMBL IDs efficiently |
calculate_descriptors | read | Calculate molecular descriptors and physicochemical properties |
compare_activities | read | Compare bioactivity data across multiple compounds or targets |
get_assay_info | read | Get detailed information for a specific assay by ChEMBL assay ID |
get_compound_info | read | Get detailed information for a specific compound by ChEMBL ID |
get_compound_structure | read | Retrieve chemical structure information in various formats |
get_dose_response | read | Get dose-response data and activity profiles for compounds |
get_drug_info | read | Get drug development status and clinical trial information |
get_external_references | read | Get links to external databases (PubChem, DrugBank, PDB, etc.) |
get_mechanism_of_action | read | Get mechanism of action and target interaction data |
get_target_compounds | read | Get compounds tested against a specific target |
get_target_info | read | Get detailed information for a specific target by ChEMBL target ID |
get_target_pathways | read | Get biological pathways associated with a target |
predict_solubility | read | Predict aqueous solubility and permeability properties |
search_activities | read | Search bioactivity measurements and assay results |
search_by_activity_type | read | Find bioactivity data by specific activity type and value range |
search_by_inchi | read | Search for compounds by InChI key or InChI string |
search_by_uniprot | read | Find ChEMBL targets by UniProt accession |
search_compounds | read | Search ChEMBL database for compounds by name, synonym, or identifier |
search_drug_indications | read | Search for therapeutic indications and disease areas |
search_drugs | read | Search for approved drugs and clinical candidates |
search_similar_compounds | read | Find chemically similar compounds using Tanimoto similarity |
search_targets | read | Search for biological targets by name or type |
substructure_search | read | Find compounds containing specific substructures |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (1 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (2)
@modelcontextprotocol/sdk, axios, @types/node, typescript
chembl-mcp-server-logo.png
Gates applied: no_behavioural_pass.
77625e6efd48full audit observations/trust-audit/mcp-server/augmented-nature__chembl.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-07 | 77625e6efd48 | SAFE | B | 89 | first audit |
Questions
What is the ChEMBL MCP server?
A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.
What tools does ChEMBL expose?
27 in total: 27 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is ChEMBL safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does ChEMBL need?
No credential environment variables were found in its source, so it appears to need none.
How does ChEMBL run?
It speaks stdio, so it runs as a local process your client starts. It is published on npm as chembl-server at 1.0.0.
How current is this page?
The grade is for one exact copy of the source (77625e6efd48), read on 2026-10-07. The repository is watched and re-audited when it changes.