Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP.
Nothing to run from here
PubChem is installed from its publisher's own source and answers where it runs, so this marketplace is not in the path of a single call. There is no address here to send one to, and a panel that pretended otherwise would be showing you an answer we made up. Install it and call it from your own client — the Installation tab has the entry for each one.
10
tools declared
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trust score
remote
at its publisher
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calls last 7d
What it does
Search the PubChem chemical database for compounds, properties, safety data and bioactivity.
Quickstart
# 1 — add it to Claude Code
claude mcp add --scope user --transport http pubchem-caseyjhand-com-pubchem-mcp https://pubchem.caseyjhand.com/mcp
# 2 — ask your agent for something these tools do
# pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image and 7 more
PubChem costs nothing on mcprush: there is no plan to choose here, no cap to set and nothing mcprush can bill you for.
Publishernot claimed
PCAll 1 server
pubchem.caseyjhand.com1 server
1 category
Collected from a public index. Nobody has claimed this account, so nothing here was written by its author — claim it if it is yours.
Installation
Where are you running it?
Every route below installs the same thing and ends at the same approval screen. Nothing here runs on your machine and nothing runs on ours: this server answers at its publisher’s own address, and what you install is the connection straight to it.
Claude Codedeclared by this listing
This is a public server: it answers at its publisher’s own address and this marketplace is not in the path. Claude Code registers it in one command; --scope user makes it available in every project. The transport below is http, read from the address; if the publisher says otherwise, swap that one word.
claude mcp add --scope user --transport http pubchem-caseyjhand-com-pubchem-mcp https://pubchem.caseyjhand.com/mcpReconnect, or start a new session, and the tools appear in the model’s tool list.
Free on mcprush, and it answers at its publisher’s own address: this marketplace is not in the path, so there is no key of ours to hold and no card to add.
What it writes
One config entry pointing straight at the publisher’s own address — this marketplace is not in the path, and nothing from this listing executes on your machine.
What you approve
10 tools, with what each one reads, writes and reaches shown before you agree — the same list on every route above. Read the tool surface.
Tool surface
What the model actually sees. Descriptions are diffed on every release — see version history.
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| searchType | string | yes | Search strategy. "identifier": name/SMILES/InChIKey lookup. "formula": molecular formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that a |
| identifierType | string | no | Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey". |
| identifiers | array | no | Required for identifier search. Array of identifiers to resolve (1-25). Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES, ["BSYNRYMUTXBXSQ-UHFFFAOYSA-N"] for inchik |
| formula | string | no | Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2"). |
| allowOtherElements | boolean | no | Formula search only. When true, includes compounds with additional elements beyond the formula. |
| query | string | no | Required for substructure/superstructure/similarity searches. A SMILES string (e.g. "CC(=O)O") or PubChem CID as a string (e.g. "2244"). |
| queryType | string | no | Required for structure/similarity searches. Format of the query: "smiles" or "cid". |
| threshold | number | no | Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90. |
| offset | integer | no | Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, subs |
| maxResults | integer | no | Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20. |
| properties | array | no | Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"]. |
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cids | array | yes | PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds. |
| properties | array | no | Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBond |
| includeDescription | boolean | no | Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetc |
| descriptionOffset | integer | no | Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous c |
| maxDescriptions | integer | no | Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3. |
| includeSynonyms | boolean | no | Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists. |
| synonymOffset | integer | no | Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read |
| maxSynonyms | integer | no | Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20. |
| includeDrugLikeness | boolean | no | Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency. |
| includeClassification | boolean | no | Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return |
Fetch a 2D structure diagram (PNG image) for a compound by CID.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| size | string | no | Image size: "small" (100x100) or "large" (300x300). Default: "large". |
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
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| format | string | no | Output format. "json" (default) returns parsed atoms and bonds. "sdf" returns the raw V2000 SDF text for passthrough to other tools. |
| includeAlternateConformerIds | boolean | no | List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false. |
| maxAtoms | integer | no | Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms. |
| maxBonds | integer | no | Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds. |
| includeRawSdf | boolean | no | For format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json". |
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| xrefTypes | array | yes | Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), Taxo |
| offset | integer | no | Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| maxPerType | integer | no | Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50. |
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cids | array | yes | PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds. |
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?".
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| outcomeFilter | string | no | Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all". |
| targetGeneId | integer | no | Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this co |
| targetAccession | string | no | Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here. |
| offset | integer | no | Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| maxResults | integer | no | Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20. |
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 record
| Parameter | Type | Required | Notes |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| kinds | array | no | Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"]. |
| offset | integer | no | Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rate |
| maxEntries | integer | no | Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10. |
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| targetType | string | yes | Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions. |
| targetQuery | string | yes | Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession). |
| offset | integer | no | Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| maxResults | integer | no | Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50. |
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.
| Parameter | Type | Required | Notes |
|---|---|---|---|
| entityType | string | yes | Entity type. Determines ID format and returned fields. |
| identifiers | array | yes | Entity identifiers (1-10). Type depends on entityType: - assay: AID (number), e.g. [1000] - gene: Gene ID (number), e.g. [1956] - protein: UniProt accession (string), e.g. ["P00533"] - taxonomy: Tax I |
Free
$0 forever
- Every tool — any call limit is its publisher’s, not ours
- No card, and mcprush charges nothing for it
- Runs at its publisher’s own address — this marketplace is not in the path
- Nothing to cap, because mcprush bills nothing
What counts against your monthly calls
| Tool | Unit | Calls used | Out of the allowance |
|---|
Nothing here is billable: mcprush charges nothing to install PubChem or to call it, at any volume.
Call allowance · this installenforced at the gateway
Monthly allowance, in calls
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Alert at 80% · then the tool returns a normal MCP error
Used this month: —
—Grade not published
No rule-by-rule report on file for this release
Two independent axes, because powerful and malicious are different questions. The grade is threat only. The capability level is blast radius, and it is never a penalty on the grade — it is priced as one subtract-only term in the score, where you can see it.
This listing is an address its publisher runs, and you connect to it directly — this marketplace is not in the path. The scanner reads packages and public source, and an address is neither. So there is no grade — not a withheld one, an unmeasured one.
Release history
This is an address its publisher runs: which release it serves is theirs to choose, so there is nothing here to pin. The history below is for reading; the current release on file is 0.6.1.
0.6.1
undated
latestNo release note was published with this version.
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no reviews yet
Who can review
One review per account, from a signed-in account that does not publish this listing. Nothing else is asked — you can say what you think before you install it. Publishers can reply once per review, and a review can be edited or deleted by whoever wrote it.
Sign in to write one
Any signed-in account that does not publish PubChem can review it, once — before installing it or after. A review from an account that has installed it is marked as one.
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Nobody has reviewed this listing. The rating on the card is the mean of the reviews written here and nothing else, so there is no rating until somebody writes the first — which takes a signed-in account that does not publish it, and nothing else.