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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, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D. Jumper J, et al. Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2. Epub 2021 Jul 15. Nature. 2021. PMID: 34265844 Free PMC article.
Through an enormous experimental effort(1-4), the structures of around 100,000 unique proteins have been determined(5), but this represents a small fraction of the billions of known protein sequences(6,7). ...Predicting the three-dimensional structure that a prot …
Through an enormous experimental effort(1-4), the structures of around 100,000 unique proteins have been determined(5), but this repr …
Highly accurate protein structure prediction for the human proteome.
Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, Figurnov M, Ronneberger O, Bates R, Kohl SAA, Potapenko A, Ballard AJ, Romera-Paredes B, Nikolov S, Jain R, Clancy E, Reiman D, Petersen S, Senior AW, Kavukcuoglu K, Birney E, Kohli P, Jumper J, Hassabis D. Tunyasuvunakool K, et al. Nature. 2021 Aug;596(7873):590-596. doi: 10.1038/s41586-021-03828-1. Epub 2021 Jul 22. Nature. 2021. PMID: 34293799 Free PMC article.
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein …
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions s …
Dense Sample Deep Learning.
Hanson SJ, Yadav V, Hanson C. Hanson SJ, et al. Neural Comput. 2024 May 10;36(6):1228-1244. doi: 10.1162/neco_a_01666. Neural Comput. 2024. PMID: 38669696
Deep learning (DL), a variant of the neural network algorithms originally proposed in the 1980s (Rumelhart et al., 1986), has made surprising progress in artificial intelligence (AI), ranging from language translation, protein folding (Jumper et al., 2021), a …
Deep learning (DL), a variant of the neural network algorithms originally proposed in the 1980s (Rumelhart et al., 1986), has made surprisin …
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.
Varadi M, Bertoni D, Magana P, Paramval U, Pidruchna I, Radhakrishnan M, Tsenkov M, Nair S, Mirdita M, Yeo J, Kovalevskiy O, Tunyasuvunakool K, Laydon A, Žídek A, Tomlinson H, Hariharan D, Abrahamson J, Green T, Jumper J, Birney E, Steinegger M, Hassabis D, Velankar S. Varadi M, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D368-D375. doi: 10.1093/nar/gkad1011. Nucleic Acids Res. 2024. PMID: 37933859 Free PMC article.
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released in 2021. …
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural b …
Artificial intelligence for microbial biotechnology: beyond the hype.
Robinson SL. Robinson SL. Microb Biotechnol. 2022 Jan;15(1):65-69. doi: 10.1111/1751-7915.13943. Epub 2021 Oct 4. Microb Biotechnol. 2022. PMID: 34606686 Free PMC article.
Perhaps the most noteworthy of these advances was Google DeepMind's AlphaFold2 algorithm which smashed records in protein structure prediction (Jumper et al., 2021, Nature, 596, 583) complemented by progress made by other research groups around the globe (Bae …
Perhaps the most noteworthy of these advances was Google DeepMind's AlphaFold2 algorithm which smashed records in protein structure p …
Applying and improving AlphaFold at CASP14.
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D. Jumper J, et al. Proteins. 2021 Dec;89(12):1711-1721. doi: 10.1002/prot.26257. Proteins. 2021. PMID: 34599769 Free PMC article.
We describe the operation and improvement of AlphaFold, the system that was entered by the team AlphaFold2 to the "human" category in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The AlphaFold system entered in CASP14 is entirely different to the …
We describe the operation and improvement of AlphaFold, the system that was entered by the team AlphaFold2 to the "human" category in the 14 …
Starting at Go: Protein structure prediction succumbs to machine learning.
Rothman JE. Rothman JE. Proc Natl Acad Sci U S A. 2023 Sep 26;120(39):e2311128120. doi: 10.1073/pnas.2311128120. Epub 2023 Sep 21. Proc Natl Acad Sci U S A. 2023. PMID: 37732752 Free PMC article.
This year's Lasker Basic Science Award recognizes the invention of AlphaFold, a revolutionary advance in the history of protein research which for the first time offers the practical ability to accurately predict the three-dimensional arrangement of amino acids in the vast …
This year's Lasker Basic Science Award recognizes the invention of AlphaFold, a revolutionary advance in the history of protein resea …
Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites.
Olanders G, Testa G, Tibo A, Nittinger E, Tyrchan C. Olanders G, et al. J Chem Inf Model. 2024 Nov 25;64(22):8481-8494. doi: 10.1021/acs.jcim.4c01475. Epub 2024 Nov 1. J Chem Inf Model. 2024. PMID: 39484820
Recently, a breakthrough in computational biology has emerged with the development of deep learning algorithms capable of predicting protein structures based on their amino acid sequences (Jumper, J., et al. Nature 2021, 596, 583. ...Nature Methods 2023, 20, …
Recently, a breakthrough in computational biology has emerged with the development of deep learning algorithms capable of predicting prot …
Guillain-Barre Syndrome and COVID-19: A case report.
Bueso T, Montalvan V, Lee J, Gomez J, Ball S, Shoustari A, Julayanont P, Jumper C. Bueso T, et al. Clin Neurol Neurosurg. 2021 Jan;200:106413. doi: 10.1016/j.clineuro.2020.106413. Epub 2020 Dec 5. Clin Neurol Neurosurg. 2021. PMID: 33338825 Free PMC article. No abstract available.
SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation.
Sanders DW, Jumper CC, Ackerman PJ, Bracha D, Donlic A, Kim H, Kenney D, Castello-Serrano I, Suzuki S, Tamura T, Tavares AH, Saeed M, Holehouse AS, Ploss A, Levental I, Douam F, Padera RF, Levy BD, Brangwynne CP. Sanders DW, et al. Elife. 2021 Apr 23;10:e65962. doi: 10.7554/eLife.65962. Elife. 2021. PMID: 33890572 Free PMC article.
11 results