What file formats are supported for downloads?

The skill supports downloading model coordinates in mmCIF/PDBx and PDB formats, as well as JSON files for confidence scores and Predicted Aligned Error (PAE) matrices.

Can I process multiple proteins at once?

Yes, the skill provides patterns for batch processing UniProt lists and downloading entire proteomes via Google Cloud Storage and BigQuery metadata.

What are pLDDT scores and why do they matter?

pLDDT measures AlphaFold's per-residue confidence. Scores above 90 indicate high accuracy suitable for detailed structural analysis, while scores below 50 suggest disordered regions.

Does this skill require a local installation of AlphaFold?

No, it interacts with the AlphaFold DB API and public datasets, allowing you to access pre-calculated predictions without running the full AlphaFold model locally.

How do I find a protein structure using this skill?

You can search by UniProt accession ID or protein name to retrieve metadata and direct download links for the corresponding AlphaFold prediction.

AlphaFold Protein Structure Database

Name: AlphaFold Protein Structure Database
Author: jimmc414

byjimmc414

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324

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Data Science & ML

Access and analyze over 200 million AI-predicted protein structures for structural biology and computational drug discovery.

The AlphaFold Database skill empowers Claude to interact with the world's most comprehensive repository of predicted protein structures. It enables researchers and developers to retrieve high-accuracy 3D models using UniProt IDs, download coordinate files in mmCIF or PDB formats, and interpret critical confidence metrics like pLDDT and Predicted Aligned Error (PAE). Designed for structural proteomics and bio-computation, this skill streamlines the integration of AlphaFold's massive dataset into automated workflows, facilitating everything from protein engineering to bulk proteome analysis via the EBI API and Google Cloud Platform.

Key Features

01Integration with Biopython for programmatic structure parsing and analysis

02Retrieve 3D protein structures using UniProt accession IDs or protein names

03Bulk data access capabilities via Google Cloud Platform and BigQuery

04324 GitHub stars

05Download atomic coordinates in standard PDB and mmCIF file formats

06Access and interpret pLDDT and PAE confidence metrics for reliability assessment

Use Cases

01Identifying potential drug binding sites and performing structure-based docking studies

02Analyzing domain architectures and residue-level stability for protein engineering

03Building structural models for proteins lacking experimental data from the PDB

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos alphafold-database

For use in Claude.ai and ChatGPT

Download Skill