Can Immune vs Protein Atlas
A side-by-side look at the Can Immune and Protein Atlas MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Can Immune for biology & bioinformatics work over a hosted endpoint; choose Protein Atlas for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Can Immune when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a remote HTTP/SSE transport.
- You want tools like
database_overview, search_genes, get_gene.
Choose Protein Atlas when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
search_genes, get_protein, top_tissues.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 55/100 · Good | 51/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Remote HTTP/SSE | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 0 |
| Directory activity | 0 views 0 installs 0 upvotes | 0 views 0 installs 0 upvotes |
| Tools | 12 | 3 |
| Full listing | View Can Immune | View Protein Atlas |
Tools & capabilities
Can Immune tools 12
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.
Protein Atlas tools 3
search_genesSearch the Human Protein Atlas for human genes/proteins by gene symbol or keyword. Returns each gene with its Ensembl gene id (needed by get_protein and top_tissues), synonyms, and description. Keyless.get_proteinGet a trimmed Human Protein Atlas profile for one protein by Ensembl gene id (e.g. "ENSG00000146648"): gene, description, protein class, biological process, molecular function, RNA tissue specificity/distribution, subcellular location, and disease involvement. Use search_genes to find the Ensembl i…top_tissuesList a protein's top-expressing human tissues by RNA expression (nTPM), highest first, for one Ensembl gene id. Use search_genes to find the Ensembl id. Keyless.
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Can Immune
{
"mcpServers": {
"can-immune": {
"url": "https://canelib.erc.monash.edu/mcp"
}
}
}
Protein Atlas
{
"mcpServers": {
"protein-atlas": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-protein-atlas"
]
}
}
}
Frequently asked questions
Can Immune is categorized under Biology & Bioinformatics and uses a remote HTTP/SSE transport. Protein Atlas belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Can Immune for biology & bioinformatics work and Protein Atlas for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Can Immune has no declared pricing — check the project's own site. Protein Atlas has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add can-immune and protein-atlas as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Can Immune has a quality signal of 55/100 (Good) with 0 views, 0 installs and 0 GitHub stars. Protein Atlas has 51/100 (Good) with 0 views, 0 installs and 0 GitHub stars.