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Improving hybrid statistical and physical forcefields through local structure enumeration.
Conway P, DiMaio F. Conway P, et al. Among authors: dimaio f. Protein Sci. 2016 Aug;25(8):1525-34. doi: 10.1002/pro.2956. Epub 2016 Jun 16. Protein Sci. 2016. PMID: 27239808 Free PMC article.
Refinement of protein structures into low-resolution density maps using rosetta.
DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. DiMaio F, et al. J Mol Biol. 2009 Sep 11;392(1):181-90. doi: 10.1016/j.jmb.2009.07.008. Epub 2009 Jul 8. J Mol Biol. 2009. PMID: 19596339 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: dimaio f. Proteins. 2009;77 Suppl 9(0 9):89-99. doi: 10.1002/prot.22540. Proteins. 2009. PMID: 19701941 Free PMC article.
Alternate states of proteins revealed by detailed energy landscape mapping.
Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Tyka MD, et al. Among authors: dimaio f. J Mol Biol. 2011 Jan 14;405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. Epub 2010 Nov 10. J Mol Biol. 2011. PMID: 21073878 Free PMC article.
Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Sgourakis NG, et al. Among authors: dimaio f. J Am Chem Soc. 2011 Apr 27;133(16):6288-98. doi: 10.1021/ja111318m. Epub 2011 Apr 5. J Am Chem Soc. 2011. PMID: 21466200 Free PMC article.
Improved molecular replacement by density- and energy-guided protein structure optimization.
DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. DiMaio F, et al. Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1. Nature. 2011. PMID: 21532589 Free PMC article.
Modeling symmetric macromolecular structures in Rosetta3.
DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. DiMaio F, et al. PLoS One. 2011;6(6):e20450. doi: 10.1371/journal.pone.0020450. Epub 2011 Jun 22. PLoS One. 2011. PMID: 21731614 Free PMC article.
Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Khatib F, DiMaio F; Foldit Contenders Group; Foldit Void Crushers Group, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D. Khatib F, et al. Among authors: dimaio f. Nat Struct Mol Biol. 2011 Sep 18;18(10):1175-7. doi: 10.1038/nsmb.2119. Nat Struct Mol Biol. 2011. PMID: 21926992 Free PMC article.
Cryo-EM model validation using independent map reconstructions.
DiMaio F, Zhang J, Chiu W, Baker D. DiMaio F, et al. Protein Sci. 2013 Jun;22(6):865-8. doi: 10.1002/pro.2267. Protein Sci. 2013. PMID: 23592445 Free PMC article.
One contact for every twelve residues allows robust and accurate topology-level protein structure modeling.
Kim DE, Dimaio F, Yu-Ruei Wang R, Song Y, Baker D. Kim DE, et al. Among authors: dimaio f. Proteins. 2014 Feb;82 Suppl 2(0 2):208-18. doi: 10.1002/prot.24374. Epub 2013 Sep 10. Proteins. 2014. PMID: 23900763 Free PMC article.
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