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Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Fleishman SJ, et al. Among authors: jacak r. J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29. J Mol Biol. 2011. PMID: 22001016 Free PMC article.
A generic program for multistate protein design.
Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B. Leaver-Fay A, et al. Among authors: jacak r. PLoS One. 2011;6(7):e20937. doi: 10.1371/journal.pone.0020937. Epub 2011 Jul 6. PLoS One. 2011. PMID: 21754981 Free PMC article.
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: jacak r. Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6. Methods Enzymol. 2011. PMID: 21187238 Free PMC article.
Scientific benchmarks for guiding macromolecular energy function improvement.
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. Leaver-Fay A, et al. Among authors: jacak r. Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0. Methods Enzymol. 2013. PMID: 23422428 Free PMC article.
The length dependence of the polyQ-mediated protein aggregation.
Barton S, Jacak R, Khare SD, Ding F, Dokholyan NV. Barton S, et al. Among authors: jacak r. J Biol Chem. 2007 Aug 31;282(35):25487-92. doi: 10.1074/jbc.M701600200. Epub 2007 Jun 25. J Biol Chem. 2007. PMID: 17591778 Free article.
Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design.
Irimia A, Serra AM, Sarkar A, Jacak R, Kalyuzhniy O, Sok D, Saye-Francisco KL, Schiffner T, Tingle R, Kubitz M, Adachi Y, Stanfield RL, Deller MC, Burton DR, Schief WR, Wilson IA. Irimia A, et al. Among authors: jacak r. PLoS Pathog. 2017 Feb 22;13(2):e1006212. doi: 10.1371/journal.ppat.1006212. eCollection 2017 Feb. PLoS Pathog. 2017. PMID: 28225819 Free PMC article.
13 results