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Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.
Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Kappel K, et al. Among authors: watkins am. Nat Methods. 2020 Jul;17(7):699-707. doi: 10.1038/s41592-020-0878-9. Epub 2020 Jul 2. Nat Methods. 2020. PMID: 32616928 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.
Geometric deep learning of RNA structure.
Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Townshend RJL, et al. Among authors: watkins am. 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. Among authors: watkins am. Nat Commun. 2022 Mar 22;13(1):1536. doi: 10.1038/s41467-022-28776-w. Nat Commun. 2022. PMID: 35318324 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. Among authors: watkins a. 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.
67 results