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Ankh-score produces better sequence alignments than AlphaFold3
Open accessPreprint — published as 10.1002/prot.70143 · Paper page
Abstract
Protein sequence alignment is one of the most fundamental procedures in bioinformatics. Due to its many downstream applications, improvements to this procedure are of great importance. We consider two revolutionary con-cepts that emerged recently as candidates for improving the state-of-the-art alignment methods: AlphaFold and protein language models such as Ankh, ProtT5 or ESM-C. Alignment improvements can come from the structural alignment of AlphaFold-predicted structures or the scoring based on the similarity of protein embeddings produced by the protein language models. Thorough comparison on many domains from BAliBASE and CDD demonstrates that the Ankh-score method produces much better sequence alignments than the structural alignments using US-align of AlphaFold3-predicted structures. Both are better than the traditional method using BLOSUM matrices. This suggests that Ankh embeddings may possess certain information that is not available in the AlphaFold3-predicted structures. The alignment software is freely available as a web server at e-score.csd.uwo.ca and as source code at github.com/lucian-ilie/E-score .
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Malec, J., Rusen, K., Golding, G. B., & Ilie, L.
- Affiliations
- Western University (CA)
- McMaster University (CA)
- Corresponding author
- Ilie, Lucian
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- openRxiv
- Published
- 2025-09-07
- Volume
- 94
- Issue
- 10
- Pages
- 1631-1643
- ISSN
- 0887-3585 (ISSN-L)
- PMC
- PMC13539653
- OpenAlex
- W7160150235
- Cited by
- 1
- References
- 1
- Citations by year
- 2026: 1
- FWCI
- 2.05
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Natural Sciences and Engineering Research Council of Canada (RGPIN 2020, rgpin-2020-05733, rgpin-2021-03978, RGPIN-2021)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- protein sequence alignment, AlphaFold3, protein language models, structural alignment, alignment scoring, BAliBASE, CDD
- MeSH terms
- Algorithms, Amino Acid Sequence, Models, Molecular, Proteins, Software, Sequence Alignment, Protein Folding, Computational Biology, Sequence Analysis, Protein, Databases, Protein
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