PubChem Integration for AI Agents
Connect your AI agent to 99 PubChem actions via MCP, A2A, or SDK, with agent authentication, tool-calling execution, and security built-in.
PubChem AI Agent Actions
99 production-ready actions for your agent to do more on PubChem.
99 Actions
Search Compounds By Name - Find PubChem compound IDs (CIDs) from a compound name or synonym.
Get Compound By SMILES - Find the CID of a compound from a SMILES string.
Get Compound By InChI - Find the CID of a compound from an InChI string.
Get Compound By SDF - Find the CID of a compound from an SDF or MOL file text.
Get Compound By InChIKey - Find the CID of a compound from its InChIKey.
Get Compound By Registry ID - Find the CID of a compound from a registry number such as a CAS number.
Search Compounds By Formula - Find compounds with a molecular formula.
Autocomplete Terms - Suggest PubChem names that start with a text fragment.
Get Compound Properties - Get computed properties such as formula, weight, SMILES and InChIKey for one or more compounds.
Get Compound Synonyms - List every name PubChem has for a compound.
Get Compound Description - Get the title and source-attributed text descriptions of a compound.
Get Compound Registry IDs - List the registry identifiers PubChem holds for a compound, such as CAS, UNII and ChEBI.
Get Compound Cross-References - Get cross-references from a compound to other databases, such as PubMed, patents and genes.
Get Related Compounds - List compounds related to a compound by parent, stereo, isotope, connectivity or tautomer.
Search Compounds By Cross-Reference - Find compounds that carry a given external cross-reference, such as a registry number or PubMed ID.
Search Compounds By Mass - Find compounds by molecular weight, exact mass or monoisotopic mass, as an exact value or a range.
Get Compound Record - Get the full structure record of one or more compounds: atoms, bonds, coordinates and properties.
Get Compound Substance IDs - List the substance IDs (SIDs) that depositors submitted for a compound.
Get Compound Assay Summary - Summarise the bioassay results recorded for a compound, one row per assay.
Get Compound Conformers - List the 3D conformer IDs PubChem has for a compound.
Get Compound Dates - Get the date PubChem first created each compound record.
Standardize Structure - Run a structure through PubChem's standardization and return the standardized record.
Similarity Search - Find compounds whose 2D structure is similar to a query structure.
Substructure Search - Find compounds that contain a query structure or SMARTS pattern.
Superstructure Search - Find compounds that are contained in a query structure.
Similarity Search 3D - Find compounds whose 3D shape and features are similar to a query structure.
Identity Search - Find compounds that are identical to a query structure under a chosen definition of identity.
Get ListKey IDs - Read a page of CIDs, SIDs or AIDs from a ListKey returned by an earlier search.
Search Substances By Name - Find PubChem substance IDs (SIDs) from a substance name or synonym.
Get Substances By Source ID - Find the substance IDs (SIDs) a source deposited under its own identifier.
List Source Substances - List every substance ID (SID) a source has deposited.
Search Substances By Cross-Reference - Find substances that carry a given external cross-reference, such as a registry number or PubMed ID.
Get Substance Record - Get the full depositor record for one or more substances.
Get Substance Synonyms - List the names a depositor gave one or more substances.
Get Substance Compound IDs - Get the compound IDs (CIDs) that one or more substances were standardized into.
Get Substance Assay IDs - List the bioassays (AIDs) that tested one or more substances.
Get Substance Assay Summary - Get a table of every bioassay result for one or more substances.
Get Substance Classification - Get the classification hierarchies PubChem places a substance in.
Get Substance Cross-References - Get cross-references from one or more substances to other databases, such as registry numbers, PubMed and patents.
Get Substance Dates - Get the deposition, modification and hold dates of one or more substances.
Get Compound Assay IDs - List the bioassays (AIDs) that tested a compound.
Get Assay Summary - Get a short summary of one or more bioassays: name, source, target and counts.
Get Assay Description - Get the full description of a bioassay: protocol, readout, targets and result columns.
Get Assay Targets - List the protein and gene targets of one or more bioassays.
Get Assay Compounds - List the compounds (CIDs) or substances (SIDs) tested in a bioassay, filtered by outcome.
Get Assay Data - Get the result data of a bioassay, optionally for chosen substances only.
Get Assay Dose Response - Get the dose-response curves of chosen substances in a bioassay.
Search Assays By Target - Find the bioassays (AIDs) that tested a protein or gene target.
Get Assay Concise - Get a table of every substance result in a bioassay, one row per substance.
Get Assay Classification - Get the classification hierarchies PubChem places a bioassay in.
Get Assay Dates - Get the deposition, modification and hold dates of one or more bioassays.
List Assays By Type - List the bioassays (AIDs) of one type, such as dose-response or confirmatory assays.
List Assays By Source - List the bioassays (AIDs) deposited by one source.
Search Assays By Activity - Find the bioassays (AIDs) that report a given activity column, such as EC50 or IC50.
Get Gene Summary - Get the summary of a gene: symbol, name, organism, description and synonyms.
Get Gene Assay IDs - List the bioassays (AIDs) that tested a gene as a target.
Get Gene Pathways - List the pathways that include a gene.
Get Gene Identifiers - List the external database identifiers PubChem holds for a gene.
Get Protein Summary - Get the summary of a protein: accession, name, organism and synonyms.
Get Protein Assay IDs - List the bioassays (AIDs) that tested a protein as a target.
Get Protein Pathways - List the pathways that include a protein.
Get Protein Identifiers - List the external database identifiers PubChem holds for a protein.
Get Pathway Summary - Get the summary of a pathway: source, name, organism and description.
Get Pathway Members - List the compounds, genes or proteins that belong to a pathway.
Get Taxonomy Summary - Get the summary of an organism: scientific name, common name, rank, lineage and synonyms.
Get Taxonomy Assay IDs - List the bioassays (AIDs) that involve an organism.
Get Taxonomy Identifiers - List the external database identifiers PubChem holds for an organism.
Get Cell Line Summary - Get the summary of a cell line: accession, name, sex, category, source tissue and organism.
Get Cell Line Assay IDs - List the bioassays (AIDs) that used a cell line.
Get Cell Line Identifiers - List the external database identifiers PubChem holds for a cell line.
List Sources - List every source that has deposited substances or bioassays into PubChem.
Get Source Table - Get the table of depositing sources with their counts, category, organization and contact details.
Get Conformer - Get one computed 3D conformer of a compound, with atom coordinates.
List Annotation Headings - List every PUG View annotation heading with the record type it applies to.
List Heading Sources - List the sources that provide annotations under one PUG View heading.
List Source Annotations - List the PUG View headings that one source provides annotations for.
Get Classification Node Members - List the PubChem records classified under one node of a classification hierarchy.
Get Periodic Table - Get the periodic table of the elements with PubChem's properties for each element.
List Identifier Types - List the external identifier types PubChem can look up in one domain.
List Compound Annotation Headings - List the annotation headings that a compound has data for.
Get Compound Annotations - Get the annotations PubChem holds for a compound, such as safety, toxicity, pharmacology and physical properties, with sources.
Get Compound Literature Links - Get PubMed search links for the literature about a compound, grouped by subheading.
Get Compound Protein Structures - List the protein structures from the PDB and MMDB that contain a compound.
Get Patent - Get the PubChem record of a patent: abstract, dates, inventors, assignee and linked chemicals, genes and proteins.
Get Record Annotations - Get the annotations PubChem holds for a substance, gene, protein, pathway, taxonomy, cell line, bioassay or element.
List Substance Annotation Headings - List the annotation headings that a substance has data for.
Get Annotations By Heading - Get every record's annotation values for one heading, with the source of each.
Get Compound Source Categories - List the sources that deposited data for a compound, grouped by category.
Get Linkouts - List the external web pages that link out from a compound, substance or bioassay record.
Get Compound QR Code - Get a QR code, as SVG text, that links to a compound's PubChem page.
Get Biologic Image - Get the image of a biologic, such as a peptide or protein sequence, as SVG text.
Get RDF Resource - Get the RDF triples PubChem holds for one resource, such as a compound, substance, bioassay or gene.
Query RDF - Query PubChem RDF with a graph name and optional filters, for example to find compounds by synonym.
Get Co-occurrences - Get literature co-occurrence scores between a chemical, gene or disease and other entities.
Get RDF Reference - Look up a literature reference in PubChem RDF by PubMed ID or DOI.
Entrez Search - Search PubChem Compound, Substance or BioAssay with an Entrez query and get the matching IDs.
Entrez Summary - Get the Entrez document summaries for PubChem Compound, Substance or BioAssay IDs.
Entrez Links - Find the records in another Entrez database that are linked to PubChem Compound, Substance or BioAssay IDs.
Entrez Database Info - Get the searchable fields, links and record count of a PubChem Entrez database.
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