biotite-mcp

biotite-mcp

MCP server that wraps core features of biotite library for structural bioinformatics.

Features

This MCP server provides access to key biotite functionality including:

Structure Analysis

• Load/Save Structures: Support for PDB, mmCIF, and MMTF formats
• Structure Information: Get detailed information about protein structures
• Distance Calculations: Calculate distances between atoms
• RMSD Calculations: Compare structures using RMSD
• Ramachandran Plots: Generate backbone dihedral angle analysis

Sequence Analysis

• Load/Save Sequences: Support for FASTA and other sequence formats
• Pairwise Alignment: Perform sequence alignments with customizable parameters
• Multiple Alignment: Support for multiple sequence alignment tools

Database Integration

• RCSB PDB: Fetch structures directly from the Protein Data Bank
• BLAST Search: Perform sequence similarity searches (requires BLAST+ installation)
• Entrez Integration: Access NCBI databases

Installation

This project uses uv for dependency management.

git clone https://github.com/antonkulaga/biotite-mcp.git
cd biotite-mcp
uv sync

Usage

As MCP Server

Configure your MCP client to use this server:

{
  "mcpServers": {
    "biotite-mcp": {
      "command": "uv",
      "args": ["run", "biotite-mcp"]
    }
  }
}

Development

Run the server in stdio mode for testing:

uv run stdio

Run tests:

# Run fast tests only
uv run pytest test/ -m "not slow and not integration"

# Run all tests
uv run pytest test/

# Run integration tests (requires network)
uv run pytest test/ -m "integration"

Available Tools

The server provides the following MCP tools (all prefixed with biotite_):

• biotite_load_structure - Load protein structures from files
• biotite_get_structure_info - Get detailed structure information
• biotite_calculate_distances - Calculate atomic distances
• biotite_calculate_rmsd - Calculate RMSD between structures
• biotite_pairwise_alignment - Perform sequence alignments
• biotite_fetch_from_rcsb - Download structures from PDB
• biotite_ramachandran_plot - Generate Ramachandran plots
• biotite_blast_search - BLAST sequence searches
• biotite_load_sequences - Load sequences from files

Requirements

• Python 3.10+
• biotite
• FastMCP
• Additional dependencies for specific features (e.g., BLAST+ for sequence searches)

Development Status

⚠️ WORK IN PROGRESS - This project is under active development.

License

This project is licensed under the same terms as the biotite library.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.