Sequence clustering confounds AlphaFold2
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
Predicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545 · see citing works
Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · cited 1× · see citing works
“Thus, randomly sampling diverse MSAs at shallow depths 11 enables more accurate, higher-confidence predictions than clustering by sequence similarity.”
Flagged first, then by citations
- Authors
- Schafer, J. W., Lee, M., Chakravarty, D., Thole, J. F., Chen, E. A., & Porter, L. L.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Porter, Lauren L.
- Venue
- Nature
- Published
- 2025-02-19
- Volume
- 638
- Issue
- 8051
- Pages
- E8-E12
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC10836070
- OpenAlex
- W4407722329
- Cited by
- 38
- References
- 5
- Citations by year
- 2026: 15 · 2025: 16 · 2024: 7
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, public-domain)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health (LM202011)
- U.S. National Library of Medicine (LM202011)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- AlphaFold2, sequence clustering, protein structure prediction, protein conformational sampling, protein folding, protein evolution, AlphaFold3, ColabFold
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