alphafold-database

npx skills add LeonChaoX/qinyan-academic-skills --skill alphafold-database --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# AlphaFold Database ## Overview AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by DeepMind and EMBL-EBI. Access structure predictions with confidence metrics, download coordinate files, retrieve bulk datasets, and integrate predictions into computational workflows. ## When to Use This Skill This skill should be used when working with AI-predicted protein structures in scenarios such as: - Retrieving protein structure predictions by UniProt ID or protein name - Downloading PDB/mmCIF coordinate files for structural analysis - Analyzing prediction confidence metrics (pLDDT, PAE) to assess reliability - Accessing bulk proteome datasets via Google Cloud Platform - Comparing predicted structures with experimental data - Performing structure-based drug discovery or protein engineering - Building structural models for proteins lacking experimental structures - Integrating AlphaFold predictions into computational pipelines ## Core Capabilities ### 1. Searching and Retrieving Predictions **Using Biopython (Recommended):** The Biopython library provides the simplest interface for retrieving AlphaFold structures: ```python f

Install gsutil
uv pip install gsutil
List available data
gsutil ls gs://public-datasets-deepmind-alphafold-v4/
Download entire proteomes (by taxonomy ID)
gsutil -m cp gs://public-datasets-deepmind-alphafold-v4/proteomes/proteome-tax_id-9606-*.tar .
Download specific files
gsutil cp gs://public-datasets-deepmind-alphafold-v4/accession_ids.csv .
Install Biopython for structure access
uv pip install biopython