🛠️ Tools Overview & Roadmap

This server provides a powerful suite of tools for accessing and analyzing protein structure data.

| Tool Name | Status | Description | | :--------------------------- | :-------------------- | :-------------------------------------------------------------------------------------------------------- | | protein_search_structures | ✅ Testing | Searches for protein structures using keywords, filters, pagination, and sorting. | | protein_get_structure | ✅ Testing | Fetches one or more protein structures by their PDB IDs, returning either full data or concise summaries. | | protein_find_similar | ✅ Testing | Finds proteins with similar sequence or structure. | | protein_track_ligands | ✅ Testing | Finds protein structures containing specific ligands, cofactors, or drugs. | | protein_compare_structures | 🟡 In Development | Performs a detailed side-by-side comparison of 2-10 protein structures. | | protein_analyze_collection | 🟡 In Development | Performs statistical analysis on the protein structure database. |

protein_search_structures

Search and discover protein structures from the Protein Data Bank (PDB) using a wide range of criteria.

Key Features:

• Free-text search for protein names, keywords, or PDB IDs.
• Filter by source organism, experimental method, and resolution.
• Pagination support for navigating large result sets.
• Returns rich metadata including title, organism, method, and resolution.

Example Use Cases:

• "Find all human kinase structures with resolution better than 2.0 Å"
• "Show me all cryo-EM structures of the SARS-CoV-2 spike protein"
• "List structures of hemoglobin from Escherichia coli"

protein_get_structure

Retrieve detailed information for specific protein structures by their PDB ID.

Key Features:

• Fetch single or multiple structures by their 4-character PDB ID.
• Choose between different data formats: mmCIF (default), PDB, PDBML, or JSON.
• Selectively include or exclude 3D coordinates, experimental data, and functional annotations.
• Provides access to atomic coordinates, chain information, and experimental details like R-factors and unit cell parameters.

Example Use Cases:

... View full README on GitHub