Structural Biology MCP Agent

An AI agent for structural biology that uses Model Context Protocol (MCP) to search, analyze, modify, and visualize protein structures from the RCSB Protein Data Bank.

Architecture

User (browser)
    |
Streamlit Chat UI (protein_chat_mcp.py)
    |
Claude AI (decides which tools to call)
    |
MCP Client (standard protocol)
    |
PDB MCP Server (pdb_mcp_server.py) ── 11 tools
    |
RCSB PDB APIs

Why MCP? MCP is a standard protocol for AI-tool communication. Instead of hardcoding tools inside the app, the MCP server exposes tools that any MCP-compatible AI client can discover and use automatically — Claude Code, Cursor, or this custom Streamlit app.

11 Tools

#	Tool	Description
1	search_structures	Search PDB by keyword, filter by method/resolution
2	get_structure_info	Get detailed metadata for a PDB ID
3	download_structure	Download PDB coordinate files
4	search_by_uniprot	Find structures linked to a UniProt accession
5	get_structure_quality	Resolution, R-factors, Ramachandran validation
6	replace_metal	Swap metals in HETATM records (e.g., Co → Zn)
7	mutate_residue	Mutate amino acids (e.g., HIS93 → SER)
8	remove_hetatm	Remove specific ligands/heteroatoms
9	remove_chain	Remove a chain from a multi-chain structure
10	list_hetatm	List all ligands/heteroatoms in a structure
11	get_modified_structure	Retrieve a modified PDB file

Demo

Ask the chat app:

"Download 1YOG, replace cobalt with zinc, and show me the structure"

Claude automatically chains 3 MCP tool calls:

1. download_structure("1YOG") → fetches PDB file
2. replace_metal("1YOG", "CO", "ZN") → swaps Co→Zn in HETATM records
3. show_structure_3d("1YOG_ZN") → renders interactive 3D viewer

Quick Start

1. Install dependencies

pip install "mcp[cli]" requests streamlit anthropic py3Dmol

2. Run the chat app

cd protein_chat
streamlit run protein_chat_mcp.py

Enter your Anthropic API key in the sidebar. Start chatting about protein structures.

3. Or use with Claude Code directly

claude mcp add pdb-server python /path/to/pdb_mcp_server.py

Then ask Claude Code: "Search PDB for cryoEM spike protein structures under 3A resolution"

Project Structure

structural-biology-mcp/
  pdb_mcp_server.py                # MCP server (11 tools)
  protein_chat/
    protein_chat_mcp.py            # Streamlit chat app (MCP client)
    .streamlit/config.toml         # Dark theme config
    requirements.txt               # Python dependencies
  PDB_MCP_Server_Tutorial.ipynb    # Tutorial notebook
  requirements.txt                 # Server dependencies

APIs Used

• RCSB PDB Data API - Structure metadata
• RCSB PDB Search API - Full-text and attribute search
• RCSB PDB Files - Coordinate file downloads

Requirements

• Python 3.10+
• mcp[cli] >= 1.0
• anthropic >= 0.40.0
• streamlit >= 1.37.0
• py3Dmol
• requests

License

MIT