Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Schema
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| search_compounds | Search PubChem database for compounds by name, CAS number, formula, or identifier |
| get_compound_info | Get detailed information for a specific compound by PubChem CID |
| search_by_smiles | Search for compounds by SMILES string (exact match) |
| search_by_inchi | Search for compounds by InChI or InChI key |
| search_by_cas_number | Search for compounds by CAS Registry Number |
| get_compound_synonyms | Get all names and synonyms for a compound |
| search_similar_compounds | Find chemically similar compounds using Tanimoto similarity |
| substructure_search | Find compounds containing a specific substructure |
| superstructure_search | Find larger compounds that contain the query structure |
| get_3d_conformers | Get 3D conformer data and structural information |
| analyze_stereochemistry | Analyze stereochemistry, chirality, and isomer information |
| get_compound_properties | Get molecular properties (MW, logP, TPSA, etc.) |
| calculate_descriptors | Calculate comprehensive molecular descriptors and fingerprints |
| predict_admet_properties | Predict ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity) |
| assess_drug_likeness | Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters |
| analyze_molecular_complexity | Analyze molecular complexity and synthetic accessibility |
| get_pharmacophore_features | Get pharmacophore features and binding site information |
| search_bioassays | Search for biological assays by target, description, or source |
| get_assay_info | Get detailed information for a specific bioassay by AID |
| get_compound_bioactivities | Get all bioassay results and activities for a compound |
| search_by_target | Find compounds tested against a specific biological target |
| compare_activity_profiles | Compare bioactivity profiles across multiple compounds |
| get_safety_data | Get GHS hazard classifications and safety information |
| get_toxicity_info | Get toxicity data including LD50, carcinogenicity, and mutagenicity |
| assess_environmental_fate | Assess environmental fate including biodegradation and bioaccumulation |
| get_regulatory_info | Get regulatory information from FDA, EPA, and international agencies |
| get_external_references | Get links to external databases (ChEMBL, DrugBank, KEGG, etc.) |
| search_patents | Search for chemical patents and intellectual property information |
| get_literature_references | Get PubMed citations and scientific literature references |
| batch_compound_lookup | Process multiple compound IDs efficiently |