AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
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.
Authors
- Oleg Kovalevskiy (ORCID: https://orcid.org/0000-0003-1106-3966)
- Augustin Žídek (ORCID: https://orcid.org/0000-0002-0748-9684)
- Shaun M. Kandathil (ORCID: https://orcid.org/0000-0002-2671-2140)
- Risha Patel (ORCID: https://orcid.org/0009-0001-8014-8536)
- Milot Mirdita (ORCID: https://orcid.org/0000-0001-8637-6719)
- Martin Steinegger (ORCID: https://orcid.org/0000-0001-8781-9753)
- Sreenath Nair
- Hamish Tomlinson
- Ian Sillitoe (ORCID: https://orcid.org/0000-0003-1091-9144)
- Nicola Bordin (ORCID: https://orcid.org/0000-0002-6568-9035)
- Sameer Velankar (ORCID: https://orcid.org/0000-0002-8439-5964)
- Christine Orengo (ORCID: https://orcid.org/0000-0002-7141-8936)
- Jennifer R. Fleming (ORCID: https://orcid.org/0000-0003-4016-8740)
- Marcelo Querino Lima Afonso (ORCID: https://orcid.org/0000-0002-9966-8187)
- Adam Midlik (ORCID: https://orcid.org/0000-0003-0455-2235)
- Andy M. Lau (ORCID: https://orcid.org/0000-0003-0572-7826)
- Mark Last (ORCID: https://orcid.org/0000-0003-0748-7918)
- David T. Jones (ORCID: https://orcid.org/0000-0001-8626-3765)
- Damian Bertoni (ORCID: https://orcid.org/0000-0001-8207-2486)
- Nick Dietrich (ORCID: https://orcid.org/0000-0001-8380-0203)
- Ahsan Tanweer (ORCID: https://orcid.org/0000-0002-4793-3700)
- Agata Laydon (ORCID: https://orcid.org/0000-0001-6499-8517)
- Maxim I. Tsenkov (ORCID: https://orcid.org/0000-0002-4870-239X)
- Ivanna Pidruchna (ORCID: https://orcid.org/0009-0001-9820-5287)
- Urmila Paramval (ORCID: https://orcid.org/0009-0001-9221-4596)
- Tim Green (ORCID: https://orcid.org/0000-0002-3227-1505)
- Paulyna Magaña (ORCID: https://orcid.org/0009-0004-1524-2966)
- Dare Kayode Lawal
- Dariusz Lasecki
Institutions
- European Bioinformatics Institute (GB)
- Seoul National University (KR)
- New Generation University College (ET)
- Google DeepMind (United Kingdom) (GB)
- Google (United Kingdom) (GB)
- Institute of Molecular Biology (AM)
- Bioinformatics Institute (RU)
- Institute of Structural and Molecular Biology (GB)
- University College London (GB)
- Institute of Molecular Biology and Genetics (UA)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-11-22
- DOI
- https://doi.org/10.1093/nar/gkaf1226
- Citations
- 11
- Primary Topic
- Protein Structure and Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 8.87