PDB

The PDB MCP server acts as a gateway to the Protein Data Bank (PDB), allowing you to access a comprehensive repository of 3D structures of proteins, nucleic acids, and complex assemblies. Developers can utilize this server to programmatically retrieve structural data and integrate it into bioinformatics applications or research tools, enabling advanced analysis and visualization of molecular structures.

Once connected to the PDB MCP server, you can interact with it by sending queries using standard HTTP methods. It's best to utilize GET requests to fetch data such as protein structures based on PDB IDs, or to search for specific sequences or structural features. Since no specific tools are documented yet, you can directly query the server's endpoints to access the various functionalities it offers.

Prerequisites

• Make sure you have Node.js installed on your machine.

Option A: Quick start with npx

If the NPM package becomes available in the future, you can quickly start with:

npx -y @Augmented-Nature/PDB-MCP-Server  

Option B: Global install alternative

You can also clone the repository directly from GitHub and run it locally:

git clone https://github.com/Augmented-Nature/PDB-MCP-Server.git  
cd PDB-MCP-Server  
npm install  
npm start  

When configuring the PDB MCP server, consider setting environment variables for optimal performance, such as PORT to specify the server port. Be aware that the server might require a stable internet connection to access the PDB database, and ensure that your queries are structured correctly to avoid errors.