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The AlphaFold Database Ages

Tsitsa, I.; Conev, A.; David, A.; Islam, S. A.; Sternberg, M. J. E.

2025-06-25 bioinformatics
10.1101/2025.06.22.660930 bioRxiv
Show abstract

The AlphaFold database provides 200M protein structures predicted by AlphaFold2 and released in 2022 from sequences in UniProt in April 2021. However, of the 20,504 full-length human structures in the AlphaFold database, 631 entries conflict with UniProt (version 2025_03 i.e. release 3 of 2025 published Jun 18, 2025); and there is a similar discrepancy for other species. This highlights how bioinformatics resources, as exemplified by the AlphaFold database can rapidly age. Time flies in bioinformatics.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Protein Science
○ 246 papers in training set
Top 0.2%
11.6%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 3%
8.6%
Similar papers in this journal
3
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 0.4%
6.5%
Similar papers in this journal
4
Database
◐ 61 papers in training set
Top 0.1%
6.5%
Similar papers in this journal
5
Scientific Reports
○ 3612 papers in training set
Top 13%
6.1%
6
Journal of Molecular Biology
○ 232 papers in training set
Top 0.3%
6.1%
Similar papers in this journal
7
PLOS Computational Biology
● 1863 papers in training set
Top 7%
5.3%
50% of probability mass above
8
Bioinformatics Advances
◐ 203 papers in training set
Top 1%
4.7%
9
Structure
○ 193 papers in training set
Top 0.6%
4.2%
10
Scientific Data
○ 209 papers in training set
Top 0.7%
3.9%
11
Proteins: Structure, Function, and Bioinformatics
○ 88 papers in training set
Top 0.5%
2.7%
12
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
2.3%
13
Nature Communications
○ 5641 papers in training set
Top 40%
2.3%
14
GigaScience
◐ 212 papers in training set
Top 2%
2.1%
15
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
1.9%
16
Communications Biology
○ 993 papers in training set
Top 15%
1.7%
17
Life Science Alliance
● 285 papers in training set
Top 4%
1.5%
18
Journal of Proteome Research
● 234 papers in training set
Top 1%
1.3%
19
Genome Biology and Evolution
◐ 338 papers in training set
Top 3%
1.1%
20
PLOS ONE
● 5266 papers in training set
Top 54%
1.1%
21
Nucleic Acids Research
◐ 1281 papers in training set
Top 12%
1.0%
22
eLife
● 5828 papers in training set
Top 64%
1.0%
23
F1000Research
○ 88 papers in training set
Top 3%
1.0%
24
Frontiers in Genetics
○ 230 papers in training set
Top 6%
0.8%
25
Frontiers in Molecular Biosciences
○ 102 papers in training set
Top 3%
0.8%
26
PeerJ
◐ 308 papers in training set
Top 11%
0.8%
27
Nature Methods
○ 385 papers in training set
Top 7%
0.8%
28
International Journal of Molecular Sciences
○ 494 papers in training set
Top 18%
0.6%
29
Biomolecules
○ 100 papers in training set
Top 4%
0.6%
30
ACS Omega
● 105 papers in training set
Top 4%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.