AlphaFold Database Access

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 predictions via BioPython or REST API, download coordinate files in multiple formats, analyze confidence metrics, and retrieve bulk proteome datasets via Google Cloud.

When to Use

• Retrieving AI-predicted protein structures by UniProt accession
• Downloading PDB/mmCIF coordinate files for structural analysis or docking
• Analyzing prediction confidence (pLDDT per-residue, PAE domain-level)
• Bulk-downloading entire proteome predictions via Google Cloud
• Comparing predicted structures with experimental PDB structures
• Building structural models for proteins lacking experimental data
• Identifying high-confidence binding sites for drug discovery
• For experimental structures only → use PDB directly
• For running AlphaFold predictions → use ColabFold or local AlphaFold

Prerequisites