tooluniverse-protein-structure-retrieval

Retrieve consolidated protein structure data from RCSB PDB, PDBe, and AlphaFold.

1.6k|244|Updated Mar 3, 2025

Search Tags:#AlphaFold #PDB #protein-structure #download-links #PDBe #structure-profile #ligands

Ready to run

npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-structure-retrieval

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: tooluniverse-protein-structure-retrieval
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/skills/tooluniverse-protein-structure-retrieval
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-structure-retrieval

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Protein researchers often struggle to locate and unify protein-structure data from multiple repositories, leading to fragmented workflows and inconsistent reports.

Core Features & Use Cases

Multi-source retrieval: fetch experimental structures from RCSB PDB, PDBe, and AlphaFold.
Disambiguation & mapping: resolve protein identity using name, UniProt, or PDB ID to prevent collisions.
Structure profiling: generate a comprehensive profile with metadata, ligands, and downloadable formats.
Use Case: compare experimental versus AlphaFold predictions to build publication-ready structure reports.

Quick Start

Use the protein structure retrieval skill to fetch the structure profile for PDB ID 4INS or UniProt P12345 and generate a comprehensive report with metadata, ligands, and download links.

Frequently Asked Questions about tooluniverse-protein-structure-retrieval

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I retrieve protein structure data using a UniProt accession?▼

To retrieve protein structure data, input a PDB ID, UniProt accession, or protein name to fetch experimental structures from RCSB PDB, PDBe, and AlphaFold. The system performs disambiguation and generates a comprehensive structure profile.

What is the best way to compare experimental PDB structures with AlphaFold predictions?▼

Comparing experimental PDB structures with AlphaFold predictions requires consolidating data from multiple repositories. This skill unifies RCSB PDB, PDBe, and AlphaFold sources, performing quality assessment and structured reporting to generate ready-to-use structure profiles.

Can I fetch protein structures from PDBe and RCSB PDB at the same time?▼

You can fetch protein structures from PDBe and RCSB PDB simultaneously. The skill performs multi-source retrieval to gather experimental structures from both repositories, along with AlphaFold data, into a single unified report.

Does protein structure retrieval work with just a protein name?▼

Protein structure retrieval does work with just a protein name. The skill features disambiguation and mapping capabilities to resolve protein identity from a name, preventing collisions and accurately fetching the correct experimental structures.

What is included in a protein structure profile report?▼

A protein structure profile report includes comprehensive metadata, ligand information, and download links. It consolidates experimental structures from RCSB PDB and PDBe, alongside AlphaFold predictions, with quality assessment for publication-ready results.

Why do I need disambiguation when downloading protein structure files?▼

You need disambiguation when downloading protein structure files to prevent identity collisions from similar names. The skill resolves the exact protein identity using UniProt accessions or PDB IDs before fetching data, ensuring you receive the correct structures.