PubChemSAFE
A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.
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 for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.
Features
🔍 Chemical Search & Retrieval (6 tools)
- search_compounds - Search by name, CAS number, formula, or identifier
- get_compound_info - Detailed compound information by CID
- search_by_smiles - Exact SMILES string matching
- search_by_inchi - InChI/InChI key search
- search_by_cas_number - CAS Registry Number lookup
- get_compound_synonyms - All names and synonyms
🧬 Structure Analysis & Similarity (5 tools)
- search_similar_compounds - Tanimoto similarity search
- substructure_search - Find compounds containing substructures
- superstructure_search - Find larger compounds containing query
- get_3d_conformers - 3D structural information
- analyze_stereochemistry - Chirality and isomer analysis
⚗️ Chemical Properties & Descriptors (6 tools)
- get_compound_properties - Molecular weight, logP, TPSA, etc.
- calculate_descriptors - Comprehensive molecular descriptors
- predict_admet_properties - ADMET predictions
- assess_drug_likeness - Lipinski Rule of Five analysis
- analyze_molecular_complexity - Synthetic accessibility
- get_pharmacophore_features - Pharmacophore mapping
🧪 Bioassay & Activity Data (5 tools)
- search_bioassays - Find biological assays
- get_assay_info - Detailed assay protocols
- get_compound_bioactivities - All activity data for compounds
- search_by_target - Find compounds tested against targets
- compare_activity_profiles - Cross-compound comparisons
⚠️ Safety & Toxicity (4 tools)
- get_safety_data - GHS hazard classifications
- get_toxicity_info - LD50, carcinoge
c66601f3abaeOBSERVED · 2026-10-08Connect
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 pubchem-server -- npx -y [email protected]
{
"mcpServers": {
"pubchem-server": {
"command": "npx",
"args": [
"-y",
"[email protected]"
]
}
}
}Exposed tools (30)
30 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
analyze_molecular_complexity | read | Analyze molecular complexity and synthetic accessibility |
analyze_stereochemistry | read | Analyze stereochemistry, chirality, and isomer information |
assess_drug_likeness | read | Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters |
assess_environmental_fate | read | Assess environmental fate including biodegradation and bioaccumulation |
batch_compound_lookup | read | Process multiple compound IDs efficiently |
calculate_descriptors | read | Calculate comprehensive molecular descriptors and fingerprints |
compare_activity_profiles | read | Compare bioactivity profiles across multiple compounds |
get_3d_conformers | read | Get 3D conformer data and structural information |
get_assay_info | read | Get detailed information for a specific bioassay by AID |
get_compound_bioactivities | read | Get all bioassay results and activities for a compound |
get_compound_info | read | Get detailed information for a specific compound by PubChem CID |
get_compound_properties | read | Get molecular properties (MW, logP, TPSA, etc.) |
get_compound_synonyms | read | Get all names and synonyms for a compound |
get_external_references | read | Get links to external databases (ChEMBL, DrugBank, KEGG, etc.) |
get_literature_references | read | Get PubMed citations and scientific literature references |
get_pharmacophore_features | read | Get pharmacophore features and binding site information |
get_regulatory_info | read | Get regulatory information from FDA, EPA, and international agencies |
get_safety_data | read | Get GHS hazard classifications and safety information |
get_toxicity_info | read | Get toxicity data including LD50, carcinogenicity, and mutagenicity |
predict_admet_properties | read | Predict ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity) |
search_bioassays | read | Search for biological assays by target, description, or source |
search_by_cas_number | read | Search for compounds by CAS Registry Number |
search_by_inchi | read | Search for compounds by InChI or InChI key |
search_by_smiles | read | Search for compounds by SMILES string (exact match) |
search_by_target | read | Find compounds tested against a specific biological target |
search_compounds | read | Search PubChem database for compounds by name, CAS number, formula, or identifier |
search_patents | read | Search for chemical patents and intellectual property information |
search_similar_compounds | read | Find chemically similar compounds using Tanimoto similarity |
substructure_search | read | Find compounds containing a specific substructure |
superstructure_search | read | Find larger compounds that contain the query structure |
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 (1)
@modelcontextprotocol/sdk, axios, @types/node, typescript
Gates applied: no_behavioural_pass.
c66601f3abaefull audit observations/trust-audit/mcp-server/augmented-nature__pubchem-1.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 |
|---|---|---|---|---|---|
| 2026-10-08 | c66601f3abae | SAFE | B | 89 | first audit |
Questions
What is the PubChem MCP server?
A comprehensive Model Context Protocol (MCP) server for accessing the PubChem chemical database. This server provides access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools.
What tools does PubChem expose?
30 in total: 30 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is PubChem 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 PubChem need?
No credential environment variables were found in its source, so it appears to need none.
How does PubChem run?
It speaks stdio, so it runs as a local process your client starts. It is published on npm as pubchem-server at 1.0.0.
How current is this page?
The grade is for one exact copy of the source (c66601f3abae), read on 2026-10-08. The repository is watched and re-audited when it changes.