Tyka MD - Search Results

1

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D. Das R, et al. Among authors: tyka md. Proteins. 2007;69 Suppl 8:118-28. doi: 10.1002/prot.21636. Proteins. 2007. PMID: 17894356

2

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Krieger E, et al. Proteins. 2009;77 Suppl 9(Suppl 9):114-22. doi: 10.1002/prot.22570. Proteins. 2009. PMID: 19768677 Free PMC article.

3

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. Proteins. 2009;77 Suppl 9(0 9):89-99. doi: 10.1002/prot.22540. Proteins. 2009. PMID: 19701941 Free PMC article.

4

Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.

Wang C, Vernon R, Lange O, Tyka M, Baker D. Wang C, et al. Protein Sci. 2010 Mar;19(3):494-506. doi: 10.1002/pro.327. Protein Sci. 2010. PMID: 20054832 Free PMC article.

5

Structure-guided forcefield optimization.

Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Song Y, et al. Proteins. 2011 Jun;79(6):1898-909. doi: 10.1002/prot.23013. Epub 2011 Apr 12. Proteins. 2011. PMID: 21488100 Free PMC article.

6

Modeling disordered regions in proteins using Rosetta.

Wang RY, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D. Wang RY, et al. PLoS One. 2011;6(7):e22060. doi: 10.1371/journal.pone.0022060. Epub 2011 Jul 29. PLoS One. 2011. PMID: 21829444 Free PMC article.

7

NMR structure determination for larger proteins using backbone-only data.

Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D. Raman S, et al. Science. 2010 Feb 19;327(5968):1014-8. doi: 10.1126/science.1183649. Epub 2010 Feb 4. Science. 2010. PMID: 20133520 Free PMC article.

8

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. Among authors: tyka md. 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.

9

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. 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.

10

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.

Tyka MD, Jung K, Baker D. Tyka MD, et al. J Comput Chem. 2012 Dec 5;33(31):2483-91. doi: 10.1002/jcc.23069. Epub 2012 Jul 27. J Comput Chem. 2012. PMID: 22847521 Free PMC article.

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