What file formats are supported for protein structures?

The skill supports downloading and parsing both mmCIF (.cif) and PDB (.pdb) coordinate files, as well as JSON-formatted confidence data.

How do I evaluate the reliability of an AlphaFold prediction?

Use the skill's guidance on pLDDT (per-residue confidence) and PAE (Predicted Aligned Error) metrics to determine which parts of a model are reliable for structural analysis.

Can I download entire species' proteomes?

Yes, the skill includes instructions for using Google Cloud Storage (gsutil) and BigQuery to perform bulk downloads and metadata queries of complete proteome datasets.

Do I need specific libraries installed to use this skill?

For full functionality, it is recommended to have Biopython, requests, numpy, and matplotlib installed in your Python environment.

How do I retrieve structures using this skill?

You can use the provided Biopython snippets or direct REST API calls to fetch protein models by their UniProt accession IDs or gene names.

AlphaFold Structure Database

Name: AlphaFold Structure Database
Author: BbgnsurfTech

byBbgnsurfTech

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Data Science & ML

Accesses and analyzes over 200 million AI-predicted protein structures from the AlphaFold database for structural biology and drug discovery.

This skill integrates the AlphaFold DB repository into Claude's workflow, allowing researchers to programmatically retrieve, download, and analyze 3D protein models. It provides specialized guidance on using Biopython and REST APIs to fetch PDB/mmCIF files, interpret critical confidence metrics like pLDDT and PAE, and perform bulk data operations via Google Cloud Platform. Whether you are conducting structure-based drug discovery, protein engineering, or modeling proteins that lack experimental data, this skill streamlines the transition from protein sequence to structural insight.

Key Features

01Automate bulk proteome downloads via Google Cloud Storage and BigQuery

02Analyze prediction confidence using pLDDT and PAE metrics

03Retrieve 3D protein structures by UniProt ID or protein name

04Download atomic coordinates in PDB and mmCIF formats

057 GitHub stars

06Programmatic integration with Biopython for structural analysis

Use Cases

01Structure-based drug discovery and target pocket identification

02Large-scale structural proteomics and evolutionary studies

03Predicting models for proteins lacking experimental crystallographic data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection alphafold-database

For use in Claude.ai and ChatGPT

Download Skill