MCP server

Protein Atlas

io.github.pipeworx-io/protein-atlas

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Human Protein Atlas (HPA) MCP — keyless.

From the maker's README Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources. Source

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 26,779 tokens per request once connected45 tools

https://gateway.pipeworx.io/protein-atlas/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 26,779 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http protein-atlas https://gateway.pipeworx.io/protein-atlas/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.protein-atlas]
url = "https://gateway.pipeworx.io/protein-atlas/mcp"

Gemini CLI

{"mcpServers":{"protein-atlas":{"httpUrl":"https://gateway.pipeworx.io/protein-atlas/mcp"}}}

Cursor

{"mcpServers":{"protein-atlas":{"url":"https://gateway.pipeworx.io/protein-atlas/mcp"}}}

VS Code

{"servers":{"protein-atlas":{"type":"http","url":"https://gateway.pipeworx.io/protein-atlas/mcp"}}}

Antigravity

agy mcp add protein-atlas https://gateway.pipeworx.io/protein-atlas/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"protein-atlas","server_url":"https://gateway.pipeworx.io/protein-atlas/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"protein-atlas","server_url":"https://gateway.pipeworx.io/protein-atlas/mcp"}

get_protein ~161 tokens
Get 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 id
search_genes ~162 tokens
Search 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.
top_tissues ~153 tokens
List 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.

Health Data
Health data: NIH grants, WHO statistics, and genetic variants
Seqbench Workbench
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
Expression Atlas
EBI Expression Atlas MCP.
String Db
STRING-DB MCP — protein-protein interaction networks.
Oliver's mTOR Atlas
Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.
Interpro
InterPro MCP (EBI) — protein family / domain / functional-site classification.
Intact
IntAct (EBI) molecular-interaction database MCP. Keyless.
AtlasClose Governance Demo
Experimental AtlasClose governance demo. Authority checks, labeled evidence, receipts, refusals.

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