can-immune

Query CAN-IMMUNE: cancer neoantigen mutations, peptides, cell lines, MHC-I binding.

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What it can do

    What data it sees

    Do you need an account

    No: the server works without sign-in

    Query CAN-IMMUNE: cancer neoantigen mutations, peptides, cell lines, MHC-I binding. Read-only.

    How to connect

    How to connect can-immune to Claude

    The server address to paste into Claude settings:

    https://canelib.erc.monash.edu/mcp

    1. Open Claude (claude.ai or the desktop app).
    2. Go to Settings → Connectors.
    3. Click Add custom connector.
    4. Paste the server address copied below into Remote MCP server URL and click Add.
    5. In a chat, click + → Connectors and switch the new connector on.

    Custom connectors are available on Free, Pro, Max, Team and Enterprise plans (Free is limited to one). On Team and Enterprise an organization Owner adds the connector first under Organization settings → Connectors.

    Authorization

    After you click Add, a sign-in window for the service opens. Sign in with your own account and approve access. Claude never sees your password.

    How to connect can-immune to ChatGPT

    The server address to paste into ChatGPT settings:

    https://canelib.erc.monash.edu/mcp

    1. Open ChatGPT in a browser (chatgpt.com). A Plus, Pro, Business, Enterprise or Edu plan is required.
    2. Turn on developer mode once: Settings → Apps → Advanced settings → Developer mode.
    3. Open Settings → Connectors and click Create.
    4. Fill in the form: Name (anything), Description (one line about what the service does), MCP server URL (copy it below).
    5. Under Authentication choose OAuth if the service requires sign-in, otherwise None. Click Create.
    6. In a new chat open + → Apps/Connectors and enable the connector.

    OpenAI has renamed this section before (Connectors → Apps/Plugins). If the label differs, search settings for "developer mode". On Business/Enterprise workspaces an admin must allow custom connectors first.

    Authorization

    On first use ChatGPT opens the service's sign-in window. Sign in and approve access.

    How to connect can-immune to Cursor

    The server address to paste into Cursor settings:

    https://canelib.erc.monash.edu/mcp

    Fastest: click Open in Cursor below and confirm the prompt.

    Manually:

    1. In Cursor open Settings → Cursor Settings → MCP and click Add new global MCP server.
    2. Paste the JSON copied below into ~/.cursor/mcp.json (per project: .cursor/mcp.json in the repo root).
    3. Save the file. The server appears in the MCP list; authorize it there if asked.

    Authorization

    If the service needs sign-in, an authorize button appears next to the server in the MCP list.

    Server tool list (12)

    Raw names from tools/list. Only developers need these.

    database_overviewGet the headline size of the CAN-IMMUNE database in one call. Returns total counts of mutations, genes, and unique mutant peptides, plus how many cell lines, tissues, and cancer types are covered, and the data sources (COSMIC, DepMap/CCLE, PubMed). Use this first to size the resource or to answer "how big is the database / how many X are there" questions. No parameters.
    search_genesFind genes by symbol or full name, ranked by how mutated they are. Matches the gene symbol OR the full gene name (partial, case-insensitive) and returns each hit with its total mutation count, unique mutant-peptide count, sample count, and UniProt accession. Use it to locate a gene before calling `get_gene`, or to rank a set of genes by mutation burden. Results are ordered by mutation count (most mutated first).
    get_geneGet the full profile for one gene by exact symbol. Returns total mutations and how they split between cell lines vs tissues, unique mutant peptides, sample and transcript counts, UniProt accession / name / reviewed status, the top ~15 recurrent mutations in that gene, and a link to the gene page. Use this after `search_genes` (or when you already know the symbol) to answer detailed questions about a single gene. Returns an error field if the symbol is not found.
    search_cell_linesFind cancer cell lines by name, ranked by mutation burden. Returns each matching cell line with its tissue of origin, cancer type, total mutations, unique mutant peptides, data sources (COSMIC / DepMap-CCLE / PubMed), and Cellosaurus ID. Covers only cell-line models (kept separate from primary tissue samples). Use before `get_cell_line` or `top_genes_in_cell_line`. Ordered by mutation count (most mutated first).
    get_cell_lineGet the full profile for one cancer cell line by exact name. Returns tissue of origin, cancer type, total mutations, unique mutant peptides and genes, data sources, Cellosaurus and DepMap model IDs, gender, category / cell type, and the top ~15 most-mutated genes in that line, plus a link to its page. Use after `search_cell_lines`, or when the exact name is known, for a deep dive on one line. Returns an error field if the name is not found.
    top_genes_in_cell_lineRank the most-mutated genes within one specific cell line. Answers "what is the top mutated gene in <cell line>" / "which genes are most altered in <cell line>". Returns genes with their mutation counts for that line, highest first, from precomputed per-cell-line stats (fast). For the whole profile of the line use `get_cell_line` instead.
    list_cancer_typesList cancer types (histology) ranked by mutation burden. Returns each cancer type / histology with its total mutations, unique samples, and unique genes, most-mutated first. Use to see which cancer types dominate the database or to pick one for further drill-down on the website.
    list_tissuesList primary tissues ranked by mutation burden. Returns each tissue (COSMIC primary-tissue samples only, kept separate from cell lines) with its total mutations, unique samples, and unique genes, most-mutated first. Use for tissue-level questions; for cell lines use `search_cell_lines`.
    get_gene_mutationsList individual mutations in a gene (a bounded sample of rows). Each row gives the CAN-IMMUNE mutation ID (CANLIB...), the amino-acid change, the CDS change, mutation type (missense / complex substitution), data source, the sample it came from, its primary site, and the mutant peptide. Ordered by mutation ID. Capped at `limit` rows (max 100) for speed - for the complete table of a heavily-mutated gene, link the user to the gene page on the website.
    get_mhc_bindingLook up a CACHED MHC-I binding prediction for a peptide + HLA allele. Returns the NetMHCpan result (best binding core, %Rank_EL, binder level SB/WB/NB, and neoepitope %Rank_Neo when computed) for predictions already stored in the cache. This tool does NOT run new predictions - it only reads cached ones; if nothing is cached it returns cached=false with a note. To generate a new prediction, use the interactive button on the mutation page of the website.
    searchSearch CAN-IMMUNE for genes and cell lines (ChatGPT connector interface). Returns {results: [{id, title, url}]} combining matching genes and cell lines, each with a stable `id` (like 'gene:TP53' or 'cell_line:MDA-MB-231'). Pass that `id` to `fetch` to retrieve the full record. This is the generic search endpoint ChatGPT expects; MCP-native clients can also use the more specific `search_genes` / `search_cell_lines` tools.
    fetchFetch the full record for an id returned by `search` (ChatGPT connector interface). Takes an id like 'gene:TP53' or 'cell_line:MDA-MB-231' and returns {id, title, text, url, metadata} where `text` is the full JSON profile (same data as get_gene / get_cell_line). Always call `search` first to obtain a valid id.