io.github.cyanheads/protein-mcp-server

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

5 6 tools GitHub

No known CVEs

No license

Actively maintained

Last commit 24d ago

Works with most clients

Transport: stdio, sse, http

6 tools · ~983 tok

Grade B · 0.5% of 200K ctx

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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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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.

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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

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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

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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 24 days ago. It has 5 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?

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

Tools

Seven tools spanning the structure-research arc — discover, fetch, find homologs, track ligands, compare, profile the corpus, and annotate — over experimental (PDB) and predicted (AlphaFold) structures from one surface:

Tool

Description

protein_search_structures

Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.

protein_get_structure

Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining.

protein_find_similar

Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession.

protein_track_ligands

Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.

protein_compare_structures

Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix.

protein_analyze_collection

Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs.

protein_get_annotations

Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms.

protein_search_structures

Federated search across experimental (PDB) and predicted (computed-model) structures via RCSB Search v2.

Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters

content_type scopes the search to experimental

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 24 days ago. It has 5 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

Tools

Tool	Description
`protein_search_structures`	Search experimental and predicted structures by free text, sequence, or organism/method/resolution filters, with optional facet breakdowns.
`protein_get_structure`	Fetch metadata and coordinate-file URLs by ID — experimental (PDB), predicted (AlphaFold), or best-available — with batch partial success and optional coordinate inlining.
`protein_find_similar`	Find sequence homologs (RCSB mmseqs2) or fold homologs (Foldseek) from a sequence, PDB ID, or UniProt accession.
`protein_track_ligands`	Resolve ligand names/formulas to component IDs, find structures containing a ligand, or map binding-site residues.
`protein_compare_structures`	Structurally align multiple structures (TM-align / jFATCAT) to a reference or as a full pairwise matrix.
`protein_analyze_collection`	Profile the PDB into distributions and trends with server-side facets — counts, histograms, timelines, and cross-tabs.
`protein_get_annotations`	Fetch UniProt features and natural variants plus InterPro domain/family memberships with GO terms.

`protein_search_structures`

Federated search across experimental (PDB) and predicted (computed-model) structures via RCSB Search v2.

Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
content_type scopes the search to experimental

... View full README on GitHub