AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage

Nucleic Acids Res. 2025 Nov 22:gkaf1226. doi: 10.1093/nar/gkaf1226. Online ahead of print.

ABSTRACT

The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL-EBI and Google DeepMind, provides open access to hundreds of millions of high-accuracy protein structure predictions, transforming research in structural biology and the wider life sciences. Since its launch, AFDB has become a widely used bioinformatics resource, integrated into major databases, visualization platforms, and analysis pipelines. Here, we report the update of the database to align with the UniProt 2025_03 release, along with a comprehensive redesign of the entry page to enhance usability, accessibility, and structural interpretation. The new design integrates annotations directly with an interactive 3D viewer and introduces dedicated domains and summary tabs. Structural coverage has also been updated to include isoforms plus underlying multiple sequence alignments. Data are available through the website, FTP, Google Cloud, and updated APIs. Together, these advances reinforce AFDB as a sustainable resource for exploring protein sequence-structure relationships.

PMID:41273079 | DOI:10.1093/nar/gkaf1226