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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: das r. 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.
Macromolecular modeling with rosetta.
Das R, Baker D. Das R, et al. Annu Rev Biochem. 2008;77:363-82. doi: 10.1146/annurev.biochem.77.062906.171838. Annu Rev Biochem. 2008. PMID: 18410248 Review.
Prospects for de novo phasing with de novo protein models.
Das R, Baker D. Das R, et al. Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):169-75. doi: 10.1107/S0907444908020039. Epub 2009 Jan 20. Acta Crystallogr D Biol Crystallogr. 2009. PMID: 19171972 Free PMC article.
Structure prediction for CASP8 with all-atom refinement using Rosetta.
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D. Raman S, et al. Among authors: das r. Proteins. 2009;77 Suppl 9(0 9):89-99. doi: 10.1002/prot.22540. Proteins. 2009. PMID: 19701941 Free PMC article.
Simultaneous prediction of protein folding and docking at high resolution.
Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Das R, et al. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18978-83. doi: 10.1073/pnas.0904407106. Epub 2009 Oct 28. Proc Natl Acad Sci U S A. 2009. PMID: 19864631 Free PMC article.
3,524 results