analyze-active-siteLABSCO SUMMARY
Two protein questions, answered from a real structural database.
The scope is deliberately narrow: look up an active site by PDB ID, or find structures tied to a disease. That is enough to stop a model inventing residue numbers, and it is the piece most biomedical chats are missing. Anything beyond those two questions — literature, structure prediction, 3-D coordinates — is roadmap, not shipped.
What it is
An MCP server that puts protein structure knowledge from the RCSB Protein Data Bank in front of a model, so it can answer structural biology questions without that data being in its training set. The server handles the API calls, formatting and error handling.
What you get
analyze-active-site— binding sites and functional residues for a protein, given a PDB IDsearch-disease-proteins— protein structures associated with a named disease or medical condition
Requirements
Node.js 20.0.0 or higher, TypeScript 5.0+, and an MCP client. There is no published package: clone the repo, npm install, npm run build, then point your client at node and the built build/index.js. No account or API key.
Setup effort
Build from source — git clone https://github.com/acashmoney/bio-mcp.git
USE CASES
01
Checking what sits in a binding pocket
Give the model a PDB ID and get back the key residues of the active site instead of a plausible-sounding guess.
02
Finding structures to start from for a disease target
Ask for proteins linked to a condition, then pull the active site of whichever structure looks worth pursuing.
2 tools
Listed in project docs. Your client may show a different list.
search-disease-proteinsBEFORE YOU INSTALL
What to know first
Tools you get
2 tools named in the project's documentation.
Requires
Node.js 20.0.0 or later
Where it runs
The documented client runs the server on your machine.
INSTALLATION
Connect your client
Server setup
TERMINAL
git clone https://github.com/acashmoney/bio-mcp.git
cd bio-mcp
npm install
npm run buildMCP Clients
Claude Desktop
CLAUDE DESKTOP · JSON
{
"mcpServers": {
"bio-mcp": {
"command": "node",
"args": [
"<YOUR_PATH_TO_BUILD>/index.js"
]
}
}
}<YOUR_PATH_TO_BUILD>/index.js is the absolute path to build/index.js inside your clone. Restart Claude Desktop.
