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. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

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 13 days ago. It has 4 GitHub stars.

io.github.cyanheads/protein-mcp-server

MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

4 6 tools GitHub

No known CVEs

No license

Actively maintained

Last commit 13d ago

Works with most clients

Transport: stdio, sse, http

6 tools · ~983 tok

Grade B · 0.5% of 200K ctx

Edit this pageView history

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"
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![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

This server provides a powerful suite of tools for accessing and analyzing protein structure data.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

Loading README…

Scored, not listed

Why this score

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

Score breakdown

65/100across 5 weighted dimensions

How we score →

0255075100

−35

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (6)

Click any tool to inspect its schema.

~983 tokens total

Community

Reviews

Be the first to review

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. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
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 13 days ago. It has 4 GitHub stars.

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Community

Discussion

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

Edit this pageView history

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"
    }
  }
}

Are you the author?

Add this badge to your README to show your security score and help users find safe servers.

Embed in your READMEAbout badges →

[![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

This server provides a powerful suite of tools for accessing and analyzing protein structure data.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

README

protein-mcp-server

A powerful Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt. Features multi-provider orchestration, comprehensive structural analysis tools, and full observability. Built for performance and scalability, with native support for serverless deployment (Cloudflare Workers).

🛠️ Tools Overview & Roadmap

This server provides a powerful suite of tools for accessing and analyzing protein structure data.

Tool Name	Status	Description
`protein_search_structures`	✅ Testing	Searches for protein structures using keywords, filters, pagination, and sorting.
`protein_get_structure`	✅ Testing	Fetches one or more protein structures by their PDB IDs, returning either full data or concise summaries.
`protein_find_similar`	✅ Testing	Finds proteins with similar sequence or structure.
`protein_track_ligands`	✅ Testing	Finds protein structures containing specific ligands, cofactors, or drugs.
`protein_compare_structures`	🟡 In Development	Performs a detailed side-by-side comparison of 2-10 protein structures.
`protein_analyze_collection`	🟡 In Development	Performs statistical analysis on the protein structure database.

`protein_search_structures`

Search and discover protein structures from the Protein Data Bank (PDB) using a wide range of criteria.

Key Features:

Free-text search for protein names, keywords, or PDB IDs.
Filter by source organism, experimental method, and resolution.
Pagination support for navigating large result sets.
Returns rich metadata including title, organism, method, and resolution.

Example Use Cases:

"Find all human kinase structures with resolution better than 2.0 Å"
"Show me all cryo-EM structures of the SARS-CoV-2 spike protein"
"List structures of hemoglobin from Escherichia coli"

`protein_get_structure`

Retrieve detailed information for specific protein structures by their PDB ID.

Key Features:

Fetch single or multiple structures by their 4-character PDB ID.
Choose between different data formats: mmCIF (default), PDB, PDBML, or JSON.
Selectively include or exclude 3D coordinates, experimental data, and functional annotations.
Provides access to atomic coordinates, chain information, and experimental details like R-factors and unit cell parameters.

Example Use Cases:

... View full README on GitHub

Loading README…

Scored, not listed

Why this score

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

Score breakdown

65/100across 5 weighted dimensions

How we score →

0255075100

−35

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (6)

Click any tool to inspect its schema.

~983 tokens total

Community

Reviews

Be the first to review

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. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
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 13 days ago. It has 4 GitHub stars.