PubChem-MCP-Server

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

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

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

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

get_safety_data

GHS hazard classifications

get_toxicity_info

LD50, carcinogenicity data

assess_environmental_fate

Biodegradation analysis

get_regulatory_info

FDA, EPA regulations

get_external_references

Links to ChEMBL, DrugBank, etc.

search_patents

Chemical patent information

get_literature_references

PubMed citations

batch_compound_lookup

Bulk processing (up to 200 compounds)