io.github.cyanheads/protein-mcp-server

protein-mcp-server

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.

6 17/wk 6 tools GitHub npm

No known CVEs

Apache-2.0 license

Actively maintained

Last commit 0d ago

Works with most clients

Transport: stdio, sse, http

6 tools · ~983 tok

Grade B · 0.5% of 200K ctx

MCPpedia last refreshed this data 4h ago

Edit this pageView history

io.github.cyanheads/protein-mcp-server is an MCP server that federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models. Its tool list has not been published yet over stdio, sse and http, requires no API key, and scores 83/100 on MCPpedia's security, maintenance and efficiency rubric.

Health Data

Step 1

Install in your client

Config is the same across clients - only the file and path differ.

Supported in Claude Desktopstdio, sse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "protein-mcp-server": {
      "env": {
        "MCP_LOG_LEVEL": "info"
      },
      "args": [
        "protein-mcp-server@latest"
      ],
      "command": "bunx"
    }
  }
}

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[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-cyanheads-protein-mcp-server)](https://mcppedia.org/s/io-github-cyanheads-protein-mcp-server)

Read me

What io.github.cyanheads/protein-mcp-server does

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models.

Test This Server

Run this in your terminal to verify the server starts. Then let us know if it worked - your result helps other developers.

npx -y 'protein-mcp-server' 2>&1 | head -1 && echo "✓ Server started successfully"

After testing, let us know if it worked:

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Scored, not listed

Why this score

Five weighted categories - click any category to see the underlying evidence.

Score breakdown

83/100across 5 weighted dimensions

How we score →

0255075100

−17

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

Checked protein-mcp-server against OSV.dev.

Inventory

Tools (6)

Click any tool to inspect its schema.

~983 tokens total

Community

Reviews

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Have you used this server?

Share your experience - it helps other developers decide.

How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is io.github.cyanheads/protein-mcp-server safe to use?: io.github.cyanheads/protein-mcp-server has no known CVEs as of the latest MCPpedia security scan. Authentication requirements were not detected automatically - check the project's documentation before connecting in a shared environment. Licensed under Apache-2.0.
How do I install io.github.cyanheads/protein-mcp-server?: io.github.cyanheads/protein-mcp-server supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can io.github.cyanheads/protein-mcp-server do?: io.github.cyanheads/protein-mcp-server provides 6 tools: protein_search_structures, protein_get_structure, protein_find_similar, protein_track_ligands, protein_compare_structures and 1 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with io.github.cyanheads/protein-mcp-server?: io.github.cyanheads/protein-mcp-server is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.
Is io.github.cyanheads/protein-mcp-server actively maintained?: io.github.cyanheads/protein-mcp-server is actively maintained - last commit was 0 days ago. It has 6 GitHub stars.

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MCP Security Weekly

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Community

Discussion

Start a conversation

Ask a question, share a tip, or report an issue.

Has anyone used this with Cursor?How do you handle auth?Any alternatives?

{ "mcpServers": { "protein-mcp-server": { "env": { "MCP_LOG_LEVEL": "info" }, "args": [ "protein-mcp-server@latest" ], "command": "bunx" } } }

Overview

Experimental (PDB) and predicted (AlphaFold) protein structures behind one surface. Search, fetch, align, and annotate structures and their ligands across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek. No API key required.

Tools

Tool

Description

protein_search_structures

Search experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets

protein_get_structure

Fetch metadata and coordinate URLs for experimental, predicted, or best-available structures

protein_find_similar

Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)

protein_track_ligands

Resolve ligands to component IDs, find structures containing one, or map its binding site

protein_compare_structures

Align structures with TM-align or jFATCAT, against a reference or all pairs

protein_analyze_collection

Profile the PDB as counts, histograms, timelines, and cross-tabs

protein_get_annotations

Fetch UniProt features and variants plus InterPro domains with GO terms

Resources

Resource

Description

pdb://{entry_id}

Experimental structure summary for a PDB entry

af://{uniprot}

AlphaFold DB predicted-structure summary for a UniProt accession

Both resources are also reachable through protein_get_structure, for clients that don't surface resources.

Skills

Skill

Description

protein-guide

Identifier forms each tool takes, author vs label chains, residue numbering, and the gates for best_available picks, sequence and Foldseek hits, ligand counts

Frequently Asked Questions

Is io.github.cyanheads/protein-mcp-server safe to use?

io.github.cyanheads/protein-mcp-server has no known CVEs as of the latest MCPpedia security scan. Authentication requirements were not detected automatically - check the project's documentation before connecting in a shared environment. Licensed under Apache-2.0.

How do I install io.github.cyanheads/protein-mcp-server?

io.github.cyanheads/protein-mcp-server supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.

What can io.github.cyanheads/protein-mcp-server do?

io.github.cyanheads/protein-mcp-server provides 6 tools: protein_search_structures, protein_get_structure, protein_find_similar, protein_track_ligands, protein_compare_structures and 1 more. See the full tools list on the server page for descriptions and parameters.

What AI clients work with io.github.cyanheads/protein-mcp-server?

io.github.cyanheads/protein-mcp-server is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.

Is io.github.cyanheads/protein-mcp-server actively maintained?

io.github.cyanheads/protein-mcp-server is actively maintained - last commit was 0 days ago. It has 6 GitHub stars.

@cyanheads/protein-mcp-server

Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.

7 Tools • 2 Resources

Public Hosted Server: https://protein.caseyjhand.com/mcp

Overview

Tools

Tool	Description
`protein_search_structures`	Search experimental and predicted structures by text, sequence, or organism/method/resolution, with optional facets
`protein_get_structure`	Fetch metadata and coordinate URLs for experimental, predicted, or best-available structures
`protein_find_similar`	Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek)
`protein_track_ligands`	Resolve ligands to component IDs, find structures containing one, or map its binding site
`protein_compare_structures`	Align structures with TM-align or jFATCAT, against a reference or all pairs
`protein_analyze_collection`	Profile the PDB as counts, histograms, timelines, and cross-tabs
`protein_get_annotations`	Fetch UniProt features and variants plus InterPro domains with GO terms

Resources

Resource	Description
`pdb://{entry_id}`	Experimental structure summary for a PDB entry
`af://{uniprot}`	AlphaFold DB predicted-structure summary for a UniProt accession

Both resources are also reachable through protein_get_structure, for clients that don't surface resources.

Skills

Skill	Description
`protein-guide`	Identifier forms each tool takes, author vs label chains, residue numbering, and the gates for `best_available` picks, sequence and Foldseek hits, ligand counts

... View full README on GitHub