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‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures
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“AlphaFold has combined numerous deep learning innovations to predict the three-dimensional (3D) structures of proteins at or near experimental scale resolution”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [3]
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“For example, in the field of biomedical research, we are now witnessing a deep learning revolution fuelled by major advances in many sub-fields, including genomics [22], proteomics [23], protein structure determination and design [12], drug design and discovery [24], and immunotherapy [20, 21].”
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“AlphaFold is a protein structure prediction program based on artificial intelligence (AI) that predict protein structures with greater accuracy than any other in silico method (39).”
BackgroundYang, W., Ge, J., Zhang, X., Zhu, W., Lin, L., Shi, Y., Xu, B., & Liu, R. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1243 · Cited by 16
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“…in the latest international “ Critical Assessment of Structure Prediction ” (CASP14) competition — the atomic coordinates of a few of its predicted structures are indistinguishable from those obtained by cryo-electron microscopy (at 0.3 – 0.6 nm resolution) of the folded proteins (Callaway, 2020).”
BackgroundInfluentialHow Similar Are Proteins and Origami?
Azulay, H., Lutaty, A., & Qvit, N. (2022) · Biomolecules · doi:10.3390/biom12050622 · Cited by 13
“For example, it was recently published that an AI program, AlphaFold2, scored above 90 (out of 100) for around two-thirds of the proteins in a challenge called Critical Assessment for Structure Prediction (CASP), which measures the degree to which a computational program predicts the final protein structure based on a…”
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“The exponential growth of structural data [14] and recent progress in protein structure prediction [15,16] make structure-based methods a promising approach to this strategy [17].”
BackgroundAchieving a ‘Good AI Society’: comparing the aims and progress of the EU and the USPreprint
Roberts, H., Cowls, J., Hine, E., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3851523 · Cited by 12
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“13 When near-native predictions of globular protein domains are readily (if not easily) available, both sequence and structural classi fi cations may adapt to incorporate predicted structures of sequence families lacking experimental structures.”
BackgroundComputational Strategies to Identify New Drug Candidates against Neuroinflammation
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An agnostic analysis of the human AlphaFold2 proteome using local protein conformations
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“…were further supported by Verify3D [LA3490: 89%, LA0620: 92%, LA1402: 90%, LA1400: 98%, and LA0591; 84% of the residues have an average 3D-1D score≥0.2] (Supplementary Figure S1) (Pontius et al., 1996; Callaway, 2020; Jumper et al., 2020; Senior et al., 2020) (Chaurasia et al., 2022a).”
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Comprehensive folding variations for protein folding
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Asatryan, B., Murray, B. A., Tadros, R., Rieder, M., Shah, R. A., Dabbagh, G. S., Landstrom, A. P., Dobner, S., Munroe, P. B., Haggerty, C. M., et al. (2024) · Journal of the American Heart Association · doi:10.1161/jaha.123.033557 · Cited by 12
“65”
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Ferruz, N., & Höcker, B. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01196-9 · Cited by 10
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“AI overcomes the limitations of docking, including the absence of some 3D protein structures and familiar binding substances [111,112].”
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“As an example, this year I discussed the protein folding problem and how it was solved with AI [15].”
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“AlphaFold2 (AF2) [14] is a DeepMind-released deep learning-based framework that can predict the 3D structure of some proteins with remarkable accuracy from primary sequences.”
BackgroundSaeki, Y., Kayanuma, M., Nitta, A., et al. (2021) · The Journal of Organic Chemistry · doi:10.1021/acs.joc.1c00849 · Cited by 9
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Bruner, W. S., & Grant, S. F. A. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1375481 · Cited by 10
“Already mentioned was the latest ESM-3 tool that is actively attempting to create new protein structures based on known sequences that could provide higher ef fi cient CRISPR proteins for genome editing (Callaway, 2024).”
BackgroundMethodInfluentialDavidovich, C., & Zhang, Q. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200238 · Cited by 9
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“Rather than zooming in on ML alone, Greif’s paper compares Deep Learning or Deep Neural Network approaches in AI as a subclass of ML with another paradigm of AI, namely Predictive Processing paradigm (Clark, 2013).”
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“2 resource [56] to solve the fundamental research problem of predicting the 3D structure”
BackgroundMethodAI-based protein models enhance the accuracy of experimentally determined protein crystal structures
Nam, K. H. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1208810 · Cited by 10
“In particular, DeepMind, a Google AI derivative, has achieved marked progress in biology with the AI network Alphafold2 to accurately predict the 3D structure of proteins (Callaway, 2020).”
BackgroundGenomics refined: AI-powered perspectives on structural analysis
Lou, Y., Deng, Z., & Gao, J. (2023) · Trends in Plant Science · doi:10.1016/j.tplants.2023.10.005 · Cited by 8
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“First one is the CASP [1] coordinated activities to get better prediction models which so far led to CASP13 and the latest CASP14 challenges towards developments of older and latest versions of AlphaFold respectively under DeepMind of Google [2].”
BackgroundArtificial intelligence in precision medicine
Siddiqui, S. S., Loganathan, S., Elangovan, V. R., & Ali, M. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-89925-3.00020-4 · Cited by 10
Ortmann, J. (2025) · Synthese · doi:10.1007/s11229-025-04930-x · Cited by 10
“[…] It’s going to require more thinking and less pipetting”, as one researcher puts it (Lupas n.d., cited in Callaway, 2020, 204).”
Balasco, N., Esposito, L., & Vitagliano, L. (2025) · Biomolecules · doi:10.3390/biom15050674 · Cited by 6
“The impressive performance of AF was announced by the most prestigious scientific journal [33,34] and by the general audience media as an achievement that revolutionized structural biology.”
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“Cells 2023; 46(2): 71-73 In 2020, AlphaFold2 protein structure prediction was presented at the 14th meeting of the Critical Assessment of Structure Prediction (CASP14) and fundamentally changed the structural biology field (Callaway, 2020; Jumper et al., 2021).”
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“Recently there has been a great advance in reading structural protein sequences by using so-called DeepMind artificial intelligence (e.g., Callaway, 2020).”
AlphaFold : un pas essentiel vers la fonction des protéines
Jordan, B. (2021) · médecine/sciences · doi:10.1051/medsci/2020281 · Cited by 6
Bongrand, P. (2022) · Current Issues in Molecular Biology · doi:10.3390/cimb44020035 · Cited by 6
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“although alphaFold2 does not provide a solution to the protein folding problem (34), it has an accuracy level comparable to that of X‐ray crystallography (35).”
BackgroundSikorska, C., & Liwo, A. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04610 · Cited by 6
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“…general sense, the development and public release of the AlphaFold artificial intelligence program by Deep Mind and an associated AlphaFill algorithm have provided extraordinary opportunities for the international plant cell wall community (Callaway 2020; Jumper et al. 2021; Hekkelman et al. 2022).”
BackgroundArtificial Intelligence Cracks a 50-Year-Old Grand Challenge in Biology
O’Neill, S. (2021) · Engineering · doi:10.1016/j.eng.2021.04.003 · Cited by 6
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“While molecular docking approaches provide one means to narrow down the set of metabolites that can act as CIs [12–14], they are limited to proteins with resolved crystal structure [15].”
BackgroundReciprocal perspective as a super learner improves drug-target interaction prediction (MUSDTI)
Dick, K., Kyrollos, D. G., Cosoreanu, E. D., Dooley, J., Fryer, J., Gordon, S. M., Kharbanda, N., Klamrowski, M. M., LaCasse, P. N. L., Leung, T. F., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-16493-9 · Cited by 4
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“It is an important step in the drug discovery stage to guide the structure and properties of drug compounds 138 .”
TBM preferred to AlphaFold 3 for functional models of insect odorant receptors
Thanu, V. C., Jabeen, A., Zographos, S. E., Taylor, P. W., & Ranganathan, S. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.08.028 · Cited by 7
“In conclusion, AF has been called a game changer achieving accuracies comparable to experimental structures, especially for rigid, well-folded globular proteins [76].”
Song, J., Sun, Q., Skirtach, A. G., & Parakhonskiy, B. V. (2025) · Advances in Colloid and Interface Science · doi:10.1016/j.cis.2025.103732 · Cited by 7
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“At the time of this book going to press the basic technology of Alpha Zero has been applied in a new form to the protein folding problem, which appears to have moved a long way toward a solution to a 50 year old scientific grand challenge (Callaway, 2020).”
BackgroundHsieh, Y.-C., Delarue, M. H., Orland, H., & Koehl, P. (2023) · Viruses · doi:10.3390/v15061366 · Cited by 6
“They are inspiring biologists to rethink the way they study the function and evolution of proteins [41–43].”
BackgroundBunyat‐zada, A. R., & Ross, A. C. (2023) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2023.102367 · Cited by 7
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“30 The alternative, the RCT, is slow, expensive and cumbersome.”
BackgroundThe brain-computer analogy—“A special issue”
Matassi, G., & Martı́nez, P. (2023) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.1099253 · Cited by 7
“…or with human intervention, mainly in fields such as writing, music, and painting (e.g., Zylinska, 2020; Jukebox, https://openai.com/blog/jukebox/), but also in scientific discovery (e.g., protein fold prediction via machine-and deep-learning techniques; see Gil et al., 2014 and Callaway, 2020).”
BackgroundZahradník, J., & Schreiber, G. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00356 · Cited by 4
Yang, M., Huang, H., Huang, L., Zhang, N., Wu, J., Yang, H., & Mu, F. (2021) · Research Square · doi:10.21203/rs.3.rs-448927/v1 · Cited by 5
Metadata
- Authors
- Callaway, E.
- Corresponding author
- Callaway, Ewen
- Venue
- Nature
- Published
- 2020-11-30
- Volume
- 588
- Issue
- 7837
- Pages
- 203-204
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3108943181
- Cited by
- 499
- References
- 0
- Citations by year
- 2026: 15 · 2025: 39 · 2024: 77 · 2023: 87 · 2022: 97 · 2021: 181 · 2020: 2
- Type
- other
- Language
- en
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- DeepMind, AlphaFold, protein structure prediction, protein 3D structure, deep learning, artificial intelligence in biology, protein folding
- MeSH terms
- Deep Learning, Models, Molecular, Protein Conformation, Proteins, Time Factors, Crystallography, X-Ray, Caspases
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