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

Area of Science:

• Structural biology
• Bioinformatics
• Computational biology

Background:

• The AlphaFold Protein Structure Database (AFDB) is a key resource for accessing protein structure predictions.
• It has been widely adopted in life sciences research and integrated into various bioinformatics tools.
• Previous versions required updates to incorporate new data and improve user experience.

Purpose of the Study:

• To update the AlphaFold Protein Structure Database (AFDB) with the latest UniProt release (2025_03).
• To redesign the AFDB entry page for improved usability, accessibility, and structural interpretation.
• To expand structural coverage and enhance data accessibility.

Main Methods:

• Database update aligning with UniProt 2025_03 release.
• Redesign of the entry page with integrated annotations and an interactive 3D viewer.
• Inclusion of isoforms and multiple sequence alignments in structural coverage.

Main Results:

• The AFDB is updated to UniProt 2025_03, providing access to millions of high-accuracy protein structure predictions.
• A redesigned entry page features integrated annotations, an interactive 3D viewer, and dedicated tabs for domains and summaries.
• Expanded structural coverage now includes isoforms and multiple sequence alignments.

Conclusions:

• The updated AFDB enhances usability and accessibility for researchers.
• The database remains a vital, sustainable resource for exploring protein sequence-structure relationships.
• New features facilitate deeper structural interpretation and data integration.