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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: ovchinnikov s. 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.
Protein structure determination using metagenome sequence data.
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Ovchinnikov S, et al. Science. 2017 Jan 20;355(6322):294-298. doi: 10.1126/science.aah4043. Science. 2017. PMID: 28104891 Free PMC article.
Applications of contact predictions to structural biology.
Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Simkovic F, et al. Among authors: ovchinnikov s. IUCrJ. 2017 Apr 18;4(Pt 3):291-300. doi: 10.1107/S2052252517005115. eCollection 2017 May 1. IUCrJ. 2017. PMID: 28512576 Free PMC article. Review.
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.
Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Schoebel S, et al. Among authors: ovchinnikov s. Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6. Nature. 2017. PMID: 28682307 Free PMC article.
116 results