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Year Number of Results
2019 2
2020 3
2021 4
2022 3
2023 4
2024 1

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17 results

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Unraveling the functional dark matter through global metagenomics.
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E; Novel Metagenome Protein Families Consortium; Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC. Pavlopoulos GA, et al. Nature. 2023 Oct;622(7983):594-602. doi: 10.1038/s41586-023-06583-7. Epub 2023 Oct 11. Nature. 2023. PMID: 37821698 Free PMC article.
De novo design of small beta barrel proteins.
Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D. Kim DE, et al. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2207974120. doi: 10.1073/pnas.2207974120. Epub 2023 Mar 10. Proc Natl Acad Sci U S A. 2023. PMID: 36897987 Free PMC article.
Cyclic peptide structure prediction and design using AlphaFold.
Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Rettie SA, et al. bioRxiv [Preprint]. 2023 Feb 26:2023.02.25.529956. doi: 10.1101/2023.02.25.529956. bioRxiv. 2023. PMID: 36865323 Free PMC article. Preprint.
A structural biology community assessment of AlphaFold2 applications.
Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. Akdel M, et al. Nat Struct Mol Biol. 2022 Nov;29(11):1056-1067. doi: 10.1038/s41594-022-00849-w. Epub 2022 Nov 7. Nat Struct Mol Biol. 2022. PMID: 36344848 Free PMC article.
Scaffolding protein functional sites using deep learning.
Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, Chun JH, Dauparas J, Bennett N, Wicky BIM, Muenks A, DiMaio F, Correia B, Ovchinnikov S, Baker D. Wang J, et al. Science. 2022 Jul 22;377(6604):387-394. doi: 10.1126/science.abn2100. Epub 2022 Jul 21. Science. 2022. PMID: 35862514 Free PMC article.
ColabFold: making protein folding accessible to all.
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. Mirdita M, et al. Nat Methods. 2022 Jun;19(6):679-682. doi: 10.1038/s41592-022-01488-1. Epub 2022 May 30. Nat Methods. 2022. PMID: 35637307 Free PMC article.
De novo protein design by deep network hallucination.
Anishchenko I, Pellock SJ, Chidyausiku TM, Ramelot TA, Ovchinnikov S, Hao J, Bafna K, Norn C, Kang A, Bera AK, DiMaio F, Carter L, Chow CM, Montelione GT, Baker D. Anishchenko I, et al. Nature. 2021 Dec;600(7889):547-552. doi: 10.1038/s41586-021-04184-w. Epub 2021 Dec 1. Nature. 2021. PMID: 34853475 Free PMC article.
Structure-based protein design with deep learning.
Ovchinnikov S, Huang PS. Ovchinnikov S, et al. Curr Opin Chem Biol. 2021 Dec;65:136-144. doi: 10.1016/j.cbpa.2021.08.004. Epub 2021 Sep 20. Curr Opin Chem Biol. 2021. PMID: 34547592 Free PMC article. Review.
17 results