Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| LOGS_DIR | No | Directory for log file storage (if LOG_OUTPUT_MODE=file). | logs/ |
| MCP_AUTH_MODE | No | Authentication mode for HTTP: jwt or oauth. | jwt |
| MCP_HTTP_HOST | No | Host address for the HTTP server (if MCP_TRANSPORT_TYPE=http). | 127.0.0.1 |
| MCP_HTTP_PORT | No | Port for the HTTP server (if MCP_TRANSPORT_TYPE=http). | 3010 |
| MCP_LOG_LEVEL | No | Logging level (debug, info, notice, warning, error, crit, alert, emerg). | info |
| LOG_OUTPUT_MODE | No | Logging output mode: file or stdout. | file |
| MCP_TRANSPORT_TYPE | No | Transport mechanism: stdio or http. | stdio |
| MCP_ALLOWED_ORIGINS | No | Comma-separated list of allowed origins for CORS (if MCP_TRANSPORT_TYPE=http). | |
| MCP_AUTH_SECRET_KEY | No | Required for jwt auth. Minimum 32-character secret key for JWT authentication. |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tasks | {
"list": {},
"cancel": {},
"requests": {
"tools": {
"call": {}
}
}
} |
| tools | {
"listChanged": true
} |
| logging | {} |
| prompts | {
"listChanged": true
} |
| resources | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| pubchem_search_compoundsA | Search PubChem for chemical compounds. Five search modes:
Optionally hydrate results with properties to avoid a follow-up details call. |
| pubchem_get_compound_detailsA | Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs. |
| pubchem_get_compound_imageA | Fetch a 2D structure diagram (PNG image) for a compound by CID. |
| pubchem_get_compound_xrefsA | Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are capped per type with total counts reported. |
| pubchem_get_compound_safetyA | Get GHS (Globally Harmonized System) hazard classification and safety data for a compound. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes). Data sourced from PubChem depositors — source attribution included. |
| pubchem_get_bioactivityA | Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target information (gene symbols, protein names), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome to focus on active results. |
| pubchem_search_assaysA | Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns assay IDs (AIDs) which can be explored further with pubchem_get_summary. |
| pubchem_get_summaryA | Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |