Protein structure prediction has reached the single-structure frontier
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Several groups suggest the default AF2 pipeline struggles to model alternative conformations.
“Several groups have suggested that the default AF2 pipeline has difficulty in modeling alternative conformations45”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [45]
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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 prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,542 · see citing works
The Energy Landscapes and Motions of Proteins
Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250 · see citing works
Mariani, V., Biasini, M., Barbato, A., & Schwede, T. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt473 · Cited by 1,138 · see citing works
Intrinsic dynamics of an enzyme underlies catalysis
Eisenmesser, E., Millet, Ó., Labeikovsky, W., Korzhnev, D., Wolf-Watz, M., Bosco, D. A., Skalicky, J., Kay, L., & Kern, D. (2005) · Nature · doi:10.1038/nature04105 · Cited by 1,057 · see citing works
CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
Zhong, E. D., Bepler, T., Berger, B., & Davis, J. H. (2021) · Nature Methods · doi:10.1038/s41592-020-01049-4 · Cited by 613 · see citing works
Structure, Dynamics, and Catalytic Function of Dihydrofolate Reductase
Schnell, J. R., Dyson, H. J., & Wright, P. E. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.33.110502.133613 · Cited by 518 · see citing works
Hidden alternative structures of proline isomerase essential for catalysis
Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D., & Alber, T. (2009) · Nature · doi:10.1038/nature08615 · Cited by 509 · see citing works
Radiation damage in macromolecular crystallography: what is it and why should we care?
Garman, E. F. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910008656 · Cited by 368 · see citing works
AlphaFold2 and the future of structural biology
Cramer, P. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00650-1 · Cited by 325 · see citing works
Advances and challenges in time-resolved macromolecular crystallography
Brändén, G., & Neutze, R. (2021) · Science · doi:10.1126/science.aba0954 · Cited by 196 · see citing works
<scp>AlphaFold2</scp> fails to predict protein fold switching
Chakravarty, D., & Porter, L. L. (2022) · Protein Science · doi:10.1002/pro.4353 · Cited by 193 · see citing works
Keedy, D. A., Kenner, L. R., Warkentin, M. A., Woldeyes, R. A., Hopkins, J. B., Thompson, M. C., Brewster, A. S., Benschoten, A. H. V., Baxter, E. L., Uervirojnangkoorn, M., et al. (2015) · eLife · doi:10.7554/elife.07574 · Cited by 191 · see citing works
New Look at Hemoglobin Allostery
Yuan, Y., Tam, M. F., Simplăceanu, V., & Ho, C. (2015) · Chemical Reviews · doi:10.1021/cr500495x · Cited by 176 · see citing works
The impact of AlphaFold2 one year on
Jones, D. T., & Thornton, J. M. (2022) · Nature Methods · doi:10.1038/s41592-021-01365-3 · Cited by 152 · see citing works
Ligand binding remodels protein side-chain conformational heterogeneity
Wankowicz, S. A. M., de Oliveira, S. H. P., Hogan, D. W., Bedem, H. V. D., & Fraser, J. S. (2022) · eLife · doi:10.7554/elife.74114 · Cited by 110 · see citing works
Retrieving functional pathways of biomolecules from single-particle snapshots
Dashti, A., Mashayekhi, G., Shekhar, M., Ben-Hail, D., Salah, S., Schwander, P., Georges, A. D., Singharoy, A., Frank, J., & Ourmazd, A. (2020) · Nature Communications · doi:10.1038/s41467-020-18403-x · Cited by 104 · see citing works
CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EM Via Deep Adversarial Learning
Gupta, H., McCann, M. T., Donati, L., & Unser, M. A. (2021) · IEEE Transactions on Computational Imaging · doi:10.1109/tci.2021.3096491 · Cited by 91 · see citing works
The protein-folding problem: Not yet solved
Moore, P. B., Hendrickson, W. A., Henderson, R. A., & Brünger, A. T. (2022) · Science · doi:10.1126/science.abn9422 · Cited by 69 · see citing works
Kondrashov, D. A., Zhang, W., Aranda, R., Stec, B., & Phillips, G. N. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21499 · Cited by 52 · see citing works
Structural biology is solved — now what?
Ourmazd, A., Moffat, K., & Lattman, E. E. (2022) · Nature Methods · doi:10.1038/s41592-021-01357-3 · Cited by 39 · see citing works
Whither structural biologists?
Kleywegt, G. J., & Velankar, S. S. (2022) · IUCrJ · doi:10.1107/s2052252522005802 · Cited by 7 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- [20]Wayment-Steele, H. K., Ovchinnikov, S., Colwell, L. & Kern, D. Preprint at bioRxiv10.1101/2022.10.17.512570 (2022).
- [22]Rosenbaum, D. et al. Preprint at arXiv10.48550/arXiv.2106.14108 (2021).
- [24]Anand, N. & Achim, T. Preprint at arXiv10.48550/arXiv.2205.15019 (2022).
Cited by
Sorted by citations
The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins
Agarwal, V., & McShan, A. C. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01638-w · Cited by 155 · see citing works
A new paradigm for applying deep learning to protein–ligand interaction prediction
Wang, Z., Wang, S., Li, Y., Guo, J., Wei, Y., Mu, Y., Zheng, L., & Li, W. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae145 · Cited by 41 · see citing works
Representing structures of the multiple conformational states of proteins
Ramelot, T. A., Tejero, R., & Montelione, G. T. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102703 · Cited by 26 · see citing works
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15
Kryshtafovych, A., Montelione, G., Rigden, D., Mesdaghi, S., Karaca, E., & Moult, J. (2023) · doi:10.22541/au.169199504.48580490/v1 · Cited by 31 · see citing works
AlphaFold Prediction of Structural Ensembles of Disordered Proteins
Brotzakis, Z. F., Zhang, S., & Vendruscolo, M. (2023) · doi:10.1101/2023.01.19.524720 · Cited by 22 · see citing works
Baselious, F., Robaa, D., & Sippl, W. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107700 · Cited by 20 · see citing works
Unifying Constraints Linking Protein Folding and Native Dynamics Decoded from AlphaFold
Zhang, Z., Ren, W., Xie, L., Zheng, Y., Guan, X., Wang, J., Li, W., & Tang, Q.-Y. (2026) · Physical Review Letters · doi:10.1103/7j2j-f8f7 · Cited by 5 · see citing works
Lopez-Mateos, D., Narang, K., & Yarov-Yarovoy, V. (2024) · doi:10.1101/2024.10.15.618559 · Cited by 5 · see citing works
- Authors
- Lane, T. J.
- Affiliations
- Deutsches Elektronen-Synchrotron DESY (DE)
- Corresponding author
- Lane, Thomas J.
- ORCID
- Lane, Thomas J.
- Venue
- Nature Methods
- Published
- 2023-01-13
- Volume
- 20
- Issue
- 2
- Pages
- 170-173
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC9839224
- OpenAlex
- W4315927151
- Cited by
- 125
- References
- 22
- Citations by year
- 2026: 16 · 2025: 23 · 2024: 57 · 2023: 29
- FWCI
- 11.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron) (submittedVersion)
- Funders
- Helmholtz Association
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein structure prediction, AlphaFold2, structural ensembles, structural uncertainty, protein folding
- MeSH terms
- Protein Conformation, Proteins
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