ZBS Index What actually exists in applied AI, with the source next to it

mcp server

pubchem-mcp-server

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

Description as published by the maintainer. Source

  • version 0.6.0
  • active
  • retrieval

active — Most recent push to the repository was 2026-07-30. Dashed tags are derived by ZBS Index from the published description, not stated by the maintainer.

What this server can do

10 functions, named and described by the server itself. Parameter names are shown because they say more about what a function does than its name usually does.

pubchem_get_bioactivity(cid, offset, maxResults, targetGeneId, outcomeFilter, targetAccession)
Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?". Required: cid.
pubchem_get_compound_3d_structure(cid, format, maxAtoms, maxBonds, includeRawSdf, includeAlternateConformerIds)
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not). Required: cid.
pubchem_get_compound_details(cids, properties, maxSynonyms, synonymOffset, includeSynonyms, maxDescriptions, descriptionOffset, includeDescription, includeDrugLikeness, includeClassification)
Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call. Required: cids.
pubchem_get_compound_image(cid, size)
Fetch a 2D structure diagram (PNG image) for a compound by CID. Required: cid.
pubchem_get_compound_interactions(cid, kinds, offset, maxEntries)
Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records. Required: cid.
pubchem_get_compound_safety(cids)
Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included. Required: cids.
pubchem_get_compound_xrefs(cid, offset, xrefTypes, maxPerType)
Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset. Required: cid, xrefTypes.
pubchem_get_summary(entityType, identifiers)
Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call. Required: entityType, identifiers.
pubchem_search_assays(offset, maxResults, targetType, targetQuery)
Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary. Required: targetType, targetQuery.
pubchem_search_compounds(query, offset, formula, queryType, threshold, maxResults, properties, searchType, identifiers, identifierType, allowOtherElements)
Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call. Required: searchType.

Last successful function declaration observed on . Source: https://pubchem.caseyjhand.com/mcp. We list what the server declared; we do not call any of these functions.

Endpoint status observed on . Source: https://pubchem.caseyjhand.com/mcp.

Signals

These are separate measurements of different things. They are deliberately not combined into one score, because a popularity number that mixes website traffic with saves and stars cannot be checked or acted on.

Signal Value What it measures Window Observed Source
GitHub stars 9 Number of GitHub accounts that bookmarked this repository since it was created. It is a bookmark count, not installs, not active users and not quality. cumulative, all time GitHub
Last commit 2026-07-30 Date of the most recent push to any branch. This is the strongest cheap indicator of whether the project is still maintained. point in time GitHub
Open issues 3 Open issues plus open pull requests, as GitHub counts them together. A high number can mean an active project or an abandoned one. as of fetch GitHub
Latest published version 0.6.0 Latest version string the maintainer published to the registry. as of fetch Model Context Protocol
Registry record last updated 2026-07-28 When the registry record was last updated by its maintainer. point in time Model Context Protocol
License Apache-2.0 Licence GitHub detected in the repository. Detection can be wrong; the LICENSE file is authoritative. as of fetch GitHub
First listed in the MCP Registry 2026-07-28 Date this server was first published to the official MCP Registry. Not a usage or quality measure. point in time Model Context Protocol
repository status active The repository exists on GitHub and is not archived. This says nothing about how recently it was worked on. as of fetch GitHub
mcp tools declared 10 tools Number of functions the server itself declared when asked to list them. This is what the server offers an agent, not a measure of how well any of them work. as of probe pubchem.caseyjhand.com
mcp endpoint status ok The server listed 10 functions when asked. as of probe pubchem.caseyjhand.com

Where to get it

Related, by what their authors tagged them

  • com.covasyn/chemistry — last commit 2026-07-31, shares cheminformatics, chemistry
    Deterministic MCP for AI agents: drug discovery, ADMET, docking, LNPs, DoE, retrosynthesis, ICH M7
  • Sounio Compiler — last commit 2026-08-06, shares scientific-computing
    Check, compile, run, and test Sounio programs locally.
  • JCGE Agent Interface — last commit 2026-05-27, shares scientific-computing
    MCP server for JCGE discovery, modeling guidance, solving, validation, and equation rendering.
  • io.github.cyanheads/chembl-mcp-server — last commit 2026-07-30, shares cheminformatics, cyanheads
    Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
  • cmxflow — last commit 2026-07-11, shares cheminformatics
    Composable, tunable cheminformatics workflows: library preparation, clustering, docking, and more.
  • io.github.cyanheads/brapi-mcp-server — last commit 2026-07-16, shares bioinformatics, cyanheads
    Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.
  • io.github.cyanheads/clinicaltrialsgov-mcp-server — last commit 2026-07-26, shares bioinformatics, cyanheads
    Search ClinicalTrials.gov — find studies, retrieve results, match patients to eligible trials.
  • io.github.cyanheads/ensembl-mcp-server — last commit 2026-07-09, shares bioinformatics, cyanheads
    Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
  • io.github.cyanheads/gnomad-genetics-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
    Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.
  • io.github.cyanheads/protein-mcp-server — last commit 2026-07-30, shares bioinformatics, cyanheads
    MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

These share tags the maintainers applied themselves, such as cheminformatics, chemistry, scientific-computing, cyanheads. Common tags like "mcp" or "ai" are ignored for this: agreeing with six hundred other projects is not a similarity.

This is not a recommendation and not a test result. It is a map of what the authors said their work is about.

Also from cyanheads

How the author describes it

Topics the maintainer set on GitHub: bioinformatics, cheminformatics, chemistry, cyanheads, llm-tools, mcp, mcp-server, pubchem, scientific-computing.

This record as data

Every field on this page, with its source and observation date, is in the catalog JSON. Fetch the whole kind at once instead of parsing this HTML.

GET /api/v1/entries/mcp_server.json

Sources

  1. cyanheads/pubchem-mcp-server on GitHub — GitHub, observed , trust tier 3.
  2. Tools declared by the MCP server at https://pubchem.caseyjhand.com/mcp — pubchem.caseyjhand.com, observed , trust tier 4.
  3. Official MCP Registry — Model Context Protocol, observed , trust tier 1.