Khare SD - Search Results

1

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.

Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Mills JH, et al. Among authors: khare sd. J Am Chem Soc. 2013 Sep 11;135(36):13393-9. doi: 10.1021/ja403503m. Epub 2013 Aug 29. J Am Chem Soc. 2013. PMID: 23924187 Free PMC article.

2

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Khare SD, Kipnis Y, Greisen P Jr, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Khare SD, et al. Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777. Nat Chem Biol. 2012. PMID: 22306579 Free PMC article.

3

Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.

Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. Richter F, et al. Among authors: khare sd. J Am Chem Soc. 2012 Oct 3;134(39):16197-206. doi: 10.1021/ja3037367. Epub 2012 Sep 21. J Am Chem Soc. 2012. PMID: 22871159 Free PMC article.

4

Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.

Hansen WA, Mills JH, Khare SD. Hansen WA, et al. Among authors: khare sd. Methods Mol Biol. 2016;1414:173-85. doi: 10.1007/978-1-4939-3569-7_10. Methods Mol Biol. 2016. PMID: 27094291

5

Computational design of ligand-binding proteins with high affinity and selectivity.

Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Tinberg CE, et al. Among authors: khare sd. Nature. 2013 Sep 12;501(7466):212-216. doi: 10.1038/nature12443. Epub 2013 Sep 4. Nature. 2013. PMID: 24005320 Free PMC article.

6

A computational method for the design of nested proteins by loop-directed domain insertion.

Blacklock KM, Yang L, Mulligan VK, Khare SD. Blacklock KM, et al. Among authors: khare sd. Proteins. 2018 Mar;86(3):354-369. doi: 10.1002/prot.25445. Epub 2018 Jan 24. Proteins. 2018. PMID: 29250820

7

De novo enzyme design using Rosetta3.

Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D. Richter F, et al. Among authors: khare sd. PLoS One. 2011;6(5):e19230. doi: 10.1371/journal.pone.0019230. Epub 2011 May 16. PLoS One. 2011. PMID: 21603656 Free PMC article.

8

MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform.

Yachnin BJ, Mulligan VK, Khare SD, Bailey-Kellogg C. Yachnin BJ, et al. Among authors: khare sd. J Chem Inf Model. 2021 May 24;61(5):2368-2382. doi: 10.1021/acs.jcim.1c00056. Epub 2021 Apr 26. J Chem Inf Model. 2021. PMID: 33900750 Free PMC article.

9

Restricted sidechain plasticity in the structures of native proteins and complexes.

Fleishman SJ, Khare SD, Koga N, Baker D. Fleishman SJ, et al. Among authors: khare sd. Protein Sci. 2011 Apr;20(4):753-7. doi: 10.1002/pro.604. Protein Sci. 2011. PMID: 21432939 Free PMC article.

10

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.

Smith RD, Damm-Ganamet KL, Dunbar JB Jr, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. Smith RD, et al. Among authors: khare sd. J Chem Inf Model. 2016 Jun 27;56(6):1022-31. doi: 10.1021/acs.jcim.5b00387. Epub 2015 Oct 9. J Chem Inf Model. 2016. PMID: 26419257 Free PMC article.

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