PubChem MCP Server
UnclaimedA 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.
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analyze_molecular_complexity
Synthetic accessibility
analyze_stereochemistry
Chirality and isomer analysis
assess_drug_likeness
Lipinski Rule of Five analysis
assess_environmental_fate
Biodegradation analysis
batch_compound_lookup
Bulk processing (up to 200 compounds)
calculate_descriptors
Comprehensive molecular descriptors
compare_activity_profiles
Cross-compound comparisons
get_3d_conformers
3D structural information
get_assay_info
Detailed assay protocols
get_compound_bioactivities
All activity data for compounds
get_compound_info
Detailed compound information by CID
get_compound_properties
Molecular weight, logP, TPSA, etc.
get_compound_synonyms
All names and synonyms
get_external_references
Links to ChEMBL, DrugBank, etc.
get_literature_references
PubMed citations
get_pharmacophore_features
Pharmacophore mapping
get_regulatory_info
FDA, EPA regulations
get_safety_data
GHS hazard classifications
get_toxicity_info
LD50, carcinogenicity data
predict_admet_properties
ADMET predictions
search_bioassays
Find biological assays
search_by_cas_number
CAS Registry Number lookup
search_by_inchi
InChI/InChI key search
search_by_smiles
Exact SMILES string matching
search_by_target
Find compounds tested against targets
search_compounds
Search by name, CAS number, formula, or identifier
search_patents
Chemical patent information
search_similar_compounds
Tanimoto similarity search
substructure_search
Find compounds containing substructures
superstructure_search
Find larger compounds containing query