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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: thompson j. Proteins. 2009;77 Suppl 9(0 9):89-99. doi: 10.1002/prot.22540. Proteins. 2009. PMID: 19701941 Free PMC article.
Rosetta in CAPRI rounds 13-19.
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Fleishman SJ, et al. Among authors: thompson j. Proteins. 2010 Nov 15;78(15):3212-8. doi: 10.1002/prot.22784. Proteins. 2010. PMID: 20597089 Free PMC article.
Structure-guided forcefield optimization.
Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Song Y, et al. Among authors: thompson j. Proteins. 2011 Jun;79(6):1898-909. doi: 10.1002/prot.23013. Epub 2011 Apr 12. Proteins. 2011. PMID: 21488100 Free PMC article.
High-resolution comparative modeling with RosettaCM.
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. Song Y, et al. Among authors: thompson j. Structure. 2013 Oct 8;21(10):1735-42. doi: 10.1016/j.str.2013.08.005. Epub 2013 Sep 12. Structure. 2013. PMID: 24035711 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: thompson 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.
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