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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: karanicolas j. 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.
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P. Leaver-Fay A, et al. Among authors: karanicolas j. Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6. Methods Enzymol. 2011. PMID: 21187238 Free PMC article.
A de novo protein binding pair by computational design and directed evolution.
Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR, Baker D. Karanicolas J, et al. Mol Cell. 2011 Apr 22;42(2):250-60. doi: 10.1016/j.molcel.2011.03.010. Epub 2011 Mar 31. Mol Cell. 2011. PMID: 21458342 Free PMC article.
Hotspot-centric de novo design of protein binders.
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D. Fleishman SJ, et al. Among authors: karanicolas j. J Mol Biol. 2011 Nov 11;413(5):1047-62. doi: 10.1016/j.jmb.2011.09.001. Epub 2011 Sep 10. J Mol Biol. 2011. PMID: 21945116 Free PMC article.
Fast docking on graphics processing units via Ray-Casting.
Khar KR, Goldschmidt L, Karanicolas J. Khar KR, et al. Among authors: karanicolas j. PLoS One. 2013 Aug 16;8(8):e70661. doi: 10.1371/journal.pone.0070661. eCollection 2013. PLoS One. 2013. PMID: 23976948 Free PMC article.
74 results