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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released in 2021. Enabled by the groundbreaking AlphaFold2 artificial intelligence (AI) system, the predictions archived in AlphaFold DB have been integrated into primary data resources such as PDB, UniProt, Ensembl, InterPro and MobiDB. Our manuscript details subsequent enh…

By the Truvace desk1 min read1 sourcePeer-reviewedTRV-2026-1205· cite & verify
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
"Predicted structure of Arabidopsis DCL4 (AlphaFold)" by LocusAndLeaf is licensed under CC BY-SA 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-sa/4.0/.

In brief

By October 2023, the authors reported that the AlphaFold Protein Structure Database had grown from 300,000 structures in 2021 to over 214 million predicted structures, enabled by AlphaFold2. The paper outlines archiving enhancements, coverage of model organisms and other curated sets, and access routes including FTP and Google Cloud Public Datasets.

The expansion matters because the predictions have been integrated into primary resources such as PDB, UniProt, Ensembl, InterPro and MobiDB, extending structural information available for biological research workflows. The source does not quantify downstream discovery outcomes or validation rates, leaving uncertainty about coverage quality across all 214 million entries.

Main points

  1. AlphaFold DB grew from initial 300k structures released in 2021 to over 214 million predicted structures by 2024 coverage described in 2023 manuscript.
  2. Predictions are enabled by the AlphaFold2 artificial intelligence system.
  3. Structures have been integrated into PDB, UniProt, Ensembl, InterPro and MobiDB.
  4. Paper details data access via FTP, Google Cloud Public Datasets, and programmatic endpoints, plus improvements to Predicted Aligned Error viewer, 3D viewer customization, and search engine.

The gain

AlphaFold DB scaled from 300k to over 214 million predicted structures and was integrated into primary resources like PDB and UniProt, expanding structure coverage for research use.

The rundown

The manuscript describes successive releases covering model organisms, global health proteomes, Swiss-Prot integration and curated protein datasets, expanding from the 2021 initial release.

Access mechanisms include direct file access via FTP, advanced queries using Google Cloud Public Datasets, and programmatic access endpoints, with added services for viewing Predicted Aligned Error and customizing the 3D viewer.

Sources

  1. Peer-reviewedNucleic Acids Research2023-10-18

The debate