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8 clients · secrets stay placeholders

JSON (mcpServers)Claude CodeCodexOpenCodeCursorVS CodeGemini CLIGoose

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

claude mcp add --transport http pubchem-mcp-server https://pubchem.caseyjhand.com/mcp

[mcp_servers.pubchem-mcp-server]
url = "https://pubchem.caseyjhand.com/mcp"

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pubchem-mcp-server": {
      "type": "remote",
      "url": "https://pubchem.caseyjhand.com/mcp",
      "enabled": true
    }
  }
}

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "type": "http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=pubchem-mcp-server&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vcHViY2hlbS5jYXNleWpoYW5kLmNvbS9tY3AifQ%3D%3D"
}

{
  "servers": {
    "pubchem-mcp-server": {
      "type": "http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

{
  "mcpServers": {
    "pubchem-mcp-server": {
      "httpUrl": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

extensions:
  "pubchem-mcp-server":
    enabled: true
    name: "pubchem-mcp-server"
    type: streamable_http
    uri: "https://pubchem.caseyjhand.com/mcp"
    timeout: 300

Quality 73 / 100needs work

protocol88 · weight 25

pass
protocol.modernsupports 2026-07-28 (server/discover)
pass
protocol.statelessanswers without a session
pass
protocol.transportstreamable HTTP
warn
protocol.list_ttltools/list declares ttlMs 0, so clients re-fetch it on every use

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygiene86 · weight 30

pass
tools.descriptionsevery tool has a description
pass
tools.description_lengthdescriptions are concise
pass
tools.schemasevery tool has an object input schema
pass
tools.annotations10 of 10 tools declare readOnlyHint or destructiveHint
fail
tools.directory_hintsno tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: pubchem_search_compounds (destructiveHint); pubchem_get_compound_image (destructiveHint); pubchem_get_compound_3d_structure (destructiveHint); …
pass
tools.token_costabout 5,862 tokens to load every tool
pass
tools.api_dumptools are not a one-to-one API dump

stability25 · weight 15

warn
stability.changes20 tool changes in 30 days
fail
stability.rug_pull1 tools kept their name but changed most of their description in 30 days; review before trusting them

dependenciesn/a · weight 15

n/a
deps.known_vulns, deps.mcp_sdk_version, deps.resolvabledeps.dev does not know @cyanheads/[email protected], @cyanheads/[email protected]

10 tools, about 5,862 tokens to load them all · tool set 3a1a8dc1d5b8 · tools last changed 2026-10-15 · checked 2026-10-20 13:17 UTC

Tool changes

2026-10-15pubchem_get_summarychangeddescription, input schema, output schema
before
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.
after · 73% of words in common
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; identifiers past that are returned in unprocessed for a follow-up call.
2026-10-15pubchem_search_assayschangedinput schema, output schema
2026-10-15pubchem_get_compound_interactionschangeddescription, input schema, output schema
before
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.
after · 71% of words in common
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. Drug-drug and target interactions come from PubChem's SDQ service, which can refuse automated requests — a refused kind is reported in failedKinds while the others still return; per-target activity is also available from pubchem_get_bioactivity.
2026-10-15pubchem_get_bioactivitychangedinput schema, output schema
2026-10-15pubchem_get_compound_safetychangeddescription, input schema, output schemameaning changed
before
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.
after · 48% of words in common
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, merged across sources, plus each source's own classification — its signal word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.
2026-10-15pubchem_get_compound_xrefschangeddescription, input schema, output schema
before
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.
after · 69% of words in common
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. PubMed IDs come highest (most recently assigned) first and the other numeric types in ascending order; string IDs keep PubChem's order.
2026-10-15pubchem_get_compound_3d_structurechangedinput schema
2026-10-15pubchem_get_compound_imagechangedinput schema
2026-10-15pubchem_get_compound_detailschangeddescription, input schema, output schema
before
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.
after · 83% of words in common
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). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.
2026-10-15pubchem_search_compoundschangeddescription, input schema, output schema
before
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.
after · 85% of words in common
Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. 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.

Showing the latest 10. Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 94 / 100

provenance80

liveness100

freshness100

hygiene100

+repository +namespace-matches-repo +reachable +uptime-100% +updated-5d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

@cyanheads/[email protected] npmthis version is not known to the dependency resolver

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

remote	auth	reachable	uptime 30d	p50	protocol	last ok
`https://pubchem.caseyjhand.com/mcp` streamable-http	none	yes	100%	184 ms	2026-07-28	2026-10-20

package	registry	version	runtime	secrets
`@cyanheads/pubchem-mcp-server`	npm	0.7.0	npx
`@cyanheads/pubchem-mcp-server`	npm	0.7.0	npx

Tools (10)

`pubchem_get_bioactivity`read-only	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?".
`pubchem_get_compound_3d_structure`read-only	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).
`pubchem_get_compound_details`read-only	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). Fetches up to 100 CIDs per call; CIDs past that are returned in unprocessed for a follow-up call.
`pubchem_get_compound_image`read-only	Fetch a 2D structure diagram (PNG image) for a compound by CID.
`pubchem_get_compound_interactions`read-only	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. Drug-drug and target interactions come from PubChem's SDQ service, which can refuse automated requests — a refused kind is reported in failedKinds while the others still return; per-target activity is also available from pubchem_get_bioactivity.
`pubchem_get_compound_safety`read-only	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, merged across sources, plus each source's own classification — its signal word, pictograms, H-codes with ECHA notifier agreement percentages, and notification counts — since sources often disagree. Reports ECHA "Not Classified" verdicts as their own status.
`pubchem_get_compound_xrefs`read-only	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. PubMed IDs come highest (most recently assigned) first and the other numeric types in ascending order; string IDs keep PubChem's order.
`pubchem_get_summary`read-only	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; identifiers past that are returned in unprocessed for a follow-up call.
`pubchem_search_assays`read-only	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.
`pubchem_search_compounds`read-only	Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. 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.

Schemas: list_tools.

Similar MCP servers

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Official server.json

{
  "name": "io.github.cyanheads/pubchem-mcp-server",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://pubchem.caseyjhand.com/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "0.7.0",
  "packages": [
    {
      "version": "0.7.0",
      "transport": {
        "type": "stdio"
      },
      "identifier": "@cyanheads/pubchem-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    },
    {
      "version": "0.7.0",
      "transport": {
        "url": "http://localhost:3010/mcp",
        "type": "streamable-http"
      },
      "identifier": "@cyanheads/pubchem-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_TRANSPORT_TYPE",
          "value": "http",
          "format": "string",
          "description": "Selects the HTTP transport."
        },
        {
          "name": "MCP_SESSION_MODE",
          "format": "string",
          "default": "stateless",
          "description": "HTTP session mode: stateless, stateful, or auto. Stateless is sufficient for PubChem; auto resolves to stateful."
        },
        {
          "name": "MCP_HTTP_HOST",
          "format": "string",
          "default": "127.0.0.1",
          "description": "The hostname for the HTTP server."
        },
        {
          "name": "MCP_HTTP_PORT",
          "format": "string",
          "default": "3010",
          "description": "The port to run the HTTP server on."
        },
        {
          "name": "MCP_HTTP_ENDPOINT_PATH",
          "format": "string",
          "default": "/mcp",
          "description": "The endpoint path for the MCP server."
        },
        {
          "name": "MCP_AUTH_MODE",
          "format": "string",
          "default": "none",
          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/cyanheads/pubchem-mcp-server",
    "source": "github"
  },
  "description": "Search PubChem compounds, properties, safety data, bioactivity, and cross-references."
}