SERVER

Protein MCP Server

Rank #2,586

io.github.cyanheads/protein-mcp-server

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

29 versions

6 GitHub stars

by cyanheads (165 servers)View repository ↗

First listed

Oct 2, 2025

Last publish date

Oct 16, 2026

PURPOSE

What you can do with Protein MCP Server

Protein MCP Server is a Model Context Protocol (MCP) server published by cyanheads. It ranks #2,586 of 151,203 active servers on MCP Toplist, and its repository has 6 GitHub stars. Protein MCP Server is listed across 3 registries — Official MCP, PulseMCP and Glama, with 29 tracked versions. It was first listed on Oct 2, 2025 and most recently updated on Oct 16, 2026.

Not verifiedMCP Toplist has not yet written a checked profile for this server, so the paragraph above is assembled from registry data only. The repository README is the authority on what it does.

CAPABILITIES AND LIMITATIONS

What Protein MCP Server can and cannot do

Not verifiedMCP Toplist has not catalogued this server's tools or limitations. The repository README lists them.

REQUIREMENTS

What you need before using Protein MCP Server

DeclaredNo credentialsNo credentials declared

The registry listing declares no required environment variables or authentication. This is declared metadata, not a verified install — the repository README is the authority.

MCP Toplist probed the public endpoint on Oct 19, 2026 and could not complete the MCP handshake (jsonrpc error). Requirements remain unverified.

Declared by Glama, last synced Oct 23, 2026. Not independently verified by MCP Toplist.

Declared in the registry install config

MCP_LOG_LEVEL · optional
MCP_TRANSPORT_TYPE · optional
MCP_HTTP_HOST · optional
MCP_HTTP_PORT · optional
MCP_HTTP_ENDPOINT_PATH · optional
MCP_AUTH_MODE · optional

Hosted endpoint declared as public.

INSTALLATION AND FIRST TASK

Connect Protein MCP Server and confirm it works

Remote · HTTP

claude mcp add --transport http protein-mcp-server https://protein.caseyjhand.com/mcp

npm package

claude mcp add protein-mcp-server -e "MCP_LOG_LEVEL=<your MCP_LOG_LEVEL>" -- npx -y @cyanheads/protein-mcp-server

Replace each placeholder with your own value before saving.

npm package

claude mcp add protein-mcp-server -e "MCP_TRANSPORT_TYPE=<your MCP_TRANSPORT_TYPE>" -e "MCP_HTTP_HOST=<your MCP_HTTP_HOST>" -e "MCP_HTTP_PORT=<your MCP_HTTP_PORT>" -e "MCP_HTTP_ENDPOINT_PATH=<your MCP_HTTP_ENDPOINT_PATH>" -e "MCP_AUTH_MODE=<your MCP_AUTH_MODE>" -e "MCP_LOG_LEVEL=<your MCP_LOG_LEVEL>" -- npx -y @cyanheads/protein-mcp-server

Replace each placeholder with your own value before saving.

Remote · HTTP

[mcp_servers.protein-mcp-server]
url = "https://protein.caseyjhand.com/mcp"

Add to ~/.codex/config.toml.

npm package

[mcp_servers.protein-mcp-server]
command = "npx"
args = ["-y", "@cyanheads/protein-mcp-server"]

[mcp_servers.protein-mcp-server.env]
MCP_LOG_LEVEL = "<your MCP_LOG_LEVEL>"

Add to ~/.codex/config.toml. Replace each placeholder with your own value before saving.

npm package

[mcp_servers.protein-mcp-server]
command = "npx"
args = ["-y", "@cyanheads/protein-mcp-server"]

[mcp_servers.protein-mcp-server.env]
MCP_TRANSPORT_TYPE = "<your MCP_TRANSPORT_TYPE>"
MCP_HTTP_HOST = "<your MCP_HTTP_HOST>"
MCP_HTTP_PORT = "<your MCP_HTTP_PORT>"
MCP_HTTP_ENDPOINT_PATH = "<your MCP_HTTP_ENDPOINT_PATH>"
MCP_AUTH_MODE = "<your MCP_AUTH_MODE>"
MCP_LOG_LEVEL = "<your MCP_LOG_LEVEL>"

Add to ~/.codex/config.toml. Replace each placeholder with your own value before saving.

Remote · HTTP

https://protein.caseyjhand.com/mcp

Settings → Connectors → “Add custom connector”, then paste this URL.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to claude_desktop_config.json (Settings → Developer → Edit Config). Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<your MCP_TRANSPORT_TYPE>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to claude_desktop_config.json (Settings → Developer → Edit Config). Replace each placeholder with your own value before saving.

Remote · HTTP

{
  "mcpServers": {
    "protein-mcp-server": {
      "url": "https://protein.caseyjhand.com/mcp"
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project).

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project). Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<your MCP_TRANSPORT_TYPE>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project). Replace each placeholder with your own value before saving.

Remote · HTTP

{
  "servers": {
    "protein-mcp-server": {
      "type": "http",
      "url": "https://protein.caseyjhand.com/mcp"
    }
  }
}

Save as .vscode/mcp.json in your workspace.

npm package

{
  "servers": {
    "protein-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Save as .vscode/mcp.json in your workspace. Replace each placeholder with your own value before saving.

npm package

{
  "servers": {
    "protein-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<your MCP_TRANSPORT_TYPE>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Save as .vscode/mcp.json in your workspace. Replace each placeholder with your own value before saving.

Remote · HTTP

{
  "mcpServers": {
    "protein-mcp-server": {
      "serverUrl": "https://protein.caseyjhand.com/mcp"
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json. Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<your MCP_TRANSPORT_TYPE>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json. Replace each placeholder with your own value before saving.

Remote · HTTP

{
  "mcpServers": {
    "protein-mcp-server": {
      "url": "https://protein.caseyjhand.com/mcp"
    }
  }
}

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/protein-mcp-server"
      ],
      "env": {
        "MCP_TRANSPORT_TYPE": "<your MCP_TRANSPORT_TYPE>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Replace each placeholder with your own value before saving.

First successful task

After adding the config, ask your client to list this server's tools. A tool list confirms the connection; an empty list or an error means the server did not start or needs credentials.

ALTERNATIVES

When to choose another server

Other servers by cyanheads

View all cyanheads servers →

No task-specific alternatives are catalogued for Protein MCP Serveryet; the list above is its publisher's other servers.

MAINTENANCE AND EVIDENCE

What changed, and when this was checked

First listed: Oct 2, 2025
Latest version published: Oct 16, 2026
Version history: 29 versions tracked (below)
Requirements evidence: MCP Toplist probed the public endpoint on Oct 19, 2026 and could not complete the MCP handshake (jsonrpc error). Requirements remain unverified.
Profile checked: Not yet — purpose, capabilities and requirements above come from registry data only
Ranking data as of: Oct 23, 2026

Registry sightings

Official MCP ↗listed since Apr 25, 2026 · still listed
PulseMCP ↗listed since Jun 4, 2026 · still listed
Glama ↗listed since Jun 4, 2026 · still listed

Do you maintain Protein MCP Server? to correct or enrich this profile.

VERSIONS

Available versions (29)

Version	Published
0.8.7	Oct 16, 2026
0.8.6	Oct 7, 2026
0.8.5	Sep 22, 2026
0.8.4	Sep 22, 2026
0.8.3	Sep 22, 2026
0.8.2	Sep 22, 2026
0.8.1	Sep 16, 2026
0.8.0	Sep 9, 2026
0.7.0	Sep 9, 2026
0.6.0	Sep 9, 2026
0.5.3	Aug 30, 2026
0.5.2	Aug 25, 2026
0.5.1	Aug 17, 2026
0.5.0	Aug 17, 2026
0.4.2	Aug 17, 2026
0.4.1	Aug 17, 2026
0.4.0	Jul 3, 2026
0.3.3	Jul 3, 2026
0.3.2	Jul 3, 2026
0.3.1	Jul 3, 2026
0.3.0	Jul 3, 2026
0.2.1	Jul 3, 2026
0.2.0	Jul 3, 2026
0.1.4	Jun 23, 2026
0.1.3	Jun 20, 2026
0.1.2	Jun 18, 2026
0.1.1	Jun 18, 2026
0.1.0	Jun 15, 2026
1.0.3	Oct 2, 2025

STANDING

#2,586of 151,203 active serversTop 5%

Ranks ahead of 148,617 of 151,203 servers on MCP Toplist.

BADGE

Show your rank

Maintain this server? Add the live rank badge to your README — it updates automatically as the leaderboard changes.

Markdown

[![MCP Toplist](https://mcptoplist.com/badge/io.github.cyanheads%2Fprotein-mcp-server.svg)](https://mcptoplist.com/server/io.github.cyanheads%2Fprotein-mcp-server)

HTML

<a href="https://mcptoplist.com/server/io.github.cyanheads%2Fprotein-mcp-server"><img src="https://mcptoplist.com/badge/io.github.cyanheads%2Fprotein-mcp-server.svg" alt="MCP Toplist: Top 5% of 151,203" /></a>

Variants: append ?metric=score or ?metric=stars to the image URL.

FAQ

Frequently asked questions

Who maintains Protein MCP Server?: Protein MCP Server is maintained by cyanheads, which publishes 165 MCP servers (2813 total versions) tracked on MCP Toplist.
Is Protein MCP Server listed on the Official MCP Registry?: Yes — Protein MCP Server is listed on the Official MCP Registry, alongside PulseMCP and Glama.
How many versions does Protein MCP Server have?: MCP Toplist tracks 29 versions of Protein MCP Server, most recently published on Oct 16, 2026.
Where can I find the source code for Protein MCP Server?: The source code for Protein MCP Server is hosted at github.com/cyanheads/protein-mcp-server.

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