ChimeraX AlphaFold MCP

Example Use Cases

• 1

  Load, visualize, and manipulate molecular structures in ChimeraX using natural language commands.

• 2

  Run AlphaFold or ESMFold predictions and incorporate predicted models into interactive ChimeraX sessions.

• 3

  Perform structural analyses—distance measurements, alignments, coloring by secondary structure—and execute Python in ChimeraX programmatically.

Description

This project exposes ChimeraX and its AlphaFold tool to Claude AI via the Model Context Protocol (MCP) and a REST interface, enabling two-way conversational control of molecular visualization and structure prediction. It supports natural-language command parsing, running AlphaFold/ESMFold workflows, executing arbitrary Python in ChimeraX, and performing structural analyses like alignments and measurements. The integration aims to simplify interactive structural biology tasks by letting users control ChimeraX and AlphaFold from Claude Desktop.