AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space

This 2022 Nucleic Acids Research paper describes the open AlphaFold Protein Structure Database — the delivery mechanism for AlphaFold2's scientific impact. The database launched with 350,000 structures covering the entire human proteome and 20 model organisms. In the expanded version described in this paper, it covers over 200 million protein structures representing virtually all catalogued proteins in UniProt. The paper documents the computational pipeline for batch prediction at scale, the quality filtering applied to distinguish high-confidence from low-confidence predictions (pLDDT scores), and the public API enabling any researcher to query structures programmatically. The database essentially gives every biology lab in the world access to structural data that would have required years of X-ray crystallography or cryo-EM experiments. Hassabis frames this as the realization of the 'AlphaFold for all' promise — making the tool's benefits universally accessible rather than only to well-funded labs. Within one year of launch, the database had been accessed by over 500,000 researchers worldwide.