biotite-mcp

biotite-mcp

3.3

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

The biotite-mcp server is designed to provide seamless access to the core functionalities of the biotite library, which is widely used in structural bioinformatics. This server facilitates the analysis of protein structures and sequences by offering a range of tools for structure analysis, sequence alignment, and database integration. It supports various file formats for loading and saving structures and sequences, making it versatile for different bioinformatics workflows. The server also integrates with external databases like the RCSB PDB and NCBI, allowing users to fetch and analyze data directly from these resources. With its focus on providing a comprehensive suite of tools for bioinformatics research, the biotite-mcp server is an invaluable resource for scientists and researchers in the field.

Features

  • Load and save protein structures in PDB, mmCIF, and MMTF formats.
  • Perform distance and RMSD calculations for structural comparison.
  • Generate Ramachandran plots for dihedral angle analysis.
  • Conduct pairwise and multiple sequence alignments.
  • Fetch structures from the RCSB PDB and perform BLAST searches.

Tools

  1. biotite_load_structure

    Load protein structures from files

  2. biotite_get_structure_info

    Get detailed structure information

  3. biotite_calculate_distances

    Calculate atomic distances

  4. biotite_calculate_rmsd

    Calculate RMSD between structures

  5. biotite_pairwise_alignment

    Perform sequence alignments

  6. biotite_fetch_from_rcsb

    Download structures from PDB

  7. biotite_ramachandran_plot

    Generate Ramachandran plots

  8. biotite_blast_search

    BLAST sequence searches

  9. biotite_load_sequences

    Load sequences from files