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Year Number of Results
2017 2
2018 10
2019 14
2020 10
2021 14
2022 8
2023 9
2024 3

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67 results

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Page 1
Geometric deep learning of RNA structure.
Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Townshend RJL, et al. Science. 2021 Aug 27;373(6558):1047-1051. doi: 10.1126/science.abe5650. Science. 2021. PMID: 34446608 Free PMC article.
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.
Leppek K, Byeon GW, Kladwang W, Wayment-Steele HK, Kerr CH, Xu AF, Kim DS, Topkar VV, Choe C, Rothschild D, Tiu GC, Wellington-Oguri R, Fujii K, Sharma E, Watkins AM, Nicol JJ, Romano J, Tunguz B, Diaz F, Cai H, Guo P, Wu J, Meng F, Shi S, Participants E, Dormitzer PR, Solórzano A, Barna M, Das R. Leppek K, et al. Nat Commun. 2022 Mar 22;13(1):1536. doi: 10.1038/s41467-022-28776-w. Nat Commun. 2022. PMID: 35318324 Free PMC article.
Evaluating riboswitch optimality.
Wayment-Steele H, Wu M, Gotrik M, Das R. Wayment-Steele H, et al. Methods Enzymol. 2019;623:417-450. doi: 10.1016/bs.mie.2019.05.028. Epub 2019 Jun 18. Methods Enzymol. 2019. PMID: 31239056 Free PMC article.
How to Kinetically Dissect an RNA Machine.
Das R, Russell R. Das R, et al. Biochemistry. 2021 Nov 23;60(46):3485-3490. doi: 10.1021/acs.biochem.1c00392. Epub 2021 Sep 7. Biochemistry. 2021. PMID: 34492193 Free PMC article.
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Leman JK, et al. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1. Nat Methods. 2020. PMID: 32483333 Free PMC article. Review.
Scientific Discovery Games for Biomedical Research.
Das R, Keep B, Washington P, Riedel-Kruse IH. Das R, et al. Annu Rev Biomed Data Sci. 2019 Jul;2(1):253-279. doi: 10.1146/annurev-biodatasci-072018-021139. Annu Rev Biomed Data Sci. 2019. PMID: 34308269 Free PMC article.
Using Rosetta for RNA homology modeling.
Watkins AM, Rangan R, Das R. Watkins AM, et al. Methods Enzymol. 2019;623:177-207. doi: 10.1016/bs.mie.2019.05.026. Epub 2019 Jun 11. Methods Enzymol. 2019. PMID: 31239046 Free PMC article.
RNA 3D Modeling with FARFAR2, Online.
Watkins AM, Das R. Watkins AM, et al. Methods Mol Biol. 2023;2586:233-249. doi: 10.1007/978-1-0716-2768-6_14. Methods Mol Biol. 2023. PMID: 36705908
67 results