MCP.Market

Protein MCP server

by cyanheads·io.github.cyanheads/protein-mcp-server·v1.0.3·6 stars
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MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

A92/100grade A
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Safety scan
A92/100

full report

Adoption
Growing

6 stars35 downloads/wk

Reviews

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If you have run it, two minutes of your experience saves the next person an afternoon.

Protein tools

No tool declarations could be read from the package source. They show once the server is installed.

Public scan report

scanner v0.1.10 · 2026-10-01 · same rubric, same numbers if you re-run it

no findings
  • Code scan1 source files scanned; 1 source files scanned25/25
  • –Live reliabilityno gateway calls yet and no remote to proben/a
  • –Tool poisoningtools not inspected (local package is not executed); not countedn/a
  • Auth qualitylocal package, no credentials required12/15
  • Maintenancelast push 9 days ago15/15
  • Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10
Overall 92/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How Protein compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
92/100
higher than 95% of 48,255 servers
GitHub stars
6
more than 85% of 28,688 servers
Downloads a week
35
more than 25% of 12,191 servers with a package

Install Protein in Claude Code, Cursor or VS Code

Runs npx -y protein-mcp-server on your machine. Read the scan report first; the gateway never runs local packages.

claude mcp add protein-mcp-server -- npx -y protein-mcp-server
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What the publisher says

From the Protein repository's README, as published. We do not edit it. Read it on GitHub

@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

Experimental (PDB) and predicted (AlphaFold) protein structures, federated behind one surface. Search, fetch, align, compare, and annotate structures and their ligands across RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek — all keyless. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.

Tools

Resources

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

Protein: common questions

Is Protein MCP server safe?
Yes, by our scan: it is graded A (92/100). Read the Protein safety report
How do I install Protein?
It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.
Does Protein need an API key?
No secret keys are declared. It reads 6 settings from the environment.
Is Protein maintained?
The last commit was 42 days ago (2026-09-22). The latest release is v1.0.3.
How does Protein compare with other MCP servers?
safety score 92/100 (higher than 95% of 48,255 servers); github stars 6 (more than 85% of 28,688 servers); downloads a week 35 (more than 25% of 12,191 servers with a package). Full comparison.

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