PubChem MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_compoundsC | Search PubChem database for compounds by name, CAS number, formula, or identifier |
| get_compound_infoC | Get detailed information for a specific compound by PubChem CID |
| search_by_smilesC | Search for compounds by SMILES string (exact match) |
| search_by_inchiB | Search for compounds by InChI or InChI key |
| search_by_cas_numberC | Search for compounds by CAS Registry Number |
| get_compound_synonymsB | Get all names and synonyms for a compound |
| search_similar_compoundsC | Find chemically similar compounds using Tanimoto similarity |
| substructure_searchB | Find compounds containing a specific substructure |
| superstructure_searchC | Find larger compounds that contain the query structure |
| get_3d_conformersC | Get 3D conformer data and structural information |
| analyze_stereochemistryC | Analyze stereochemistry, chirality, and isomer information |
| get_compound_propertiesC | Get molecular properties (MW, logP, TPSA, etc.) |
| calculate_descriptorsC | Calculate comprehensive molecular descriptors and fingerprints |
| predict_admet_propertiesC | Predict ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity) |
| assess_drug_likenessC | Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters |
| analyze_molecular_complexityC | Analyze molecular complexity and synthetic accessibility |
| get_pharmacophore_featuresC | Get pharmacophore features and binding site information |
| search_bioassaysC | Search for biological assays by target, description, or source |
| get_assay_infoC | Get detailed information for a specific bioassay by AID |
| get_compound_bioactivitiesC | Get all bioassay results and activities for a compound |
| search_by_targetC | Find compounds tested against a specific biological target |
| compare_activity_profilesC | Compare bioactivity profiles across multiple compounds |
| get_safety_dataC | Get GHS hazard classifications and safety information |
| get_toxicity_infoB | Get toxicity data including LD50, carcinogenicity, and mutagenicity |
| assess_environmental_fateC | Assess environmental fate including biodegradation and bioaccumulation |
| get_regulatory_infoC | Get regulatory information from FDA, EPA, and international agencies |
| get_external_referencesC | Get links to external databases (ChEMBL, DrugBank, KEGG, etc.) |
| search_patentsC | Search for chemical patents and intellectual property information |
| get_literature_referencesC | Get PubMed citations and scientific literature references |
| batch_compound_lookupC | Process multiple compound IDs efficiently |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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