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Items: 9

1.

Massively parallel de novo protein design for targeted therapeutics.

Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, Jenkins CM, Colvin T, Carter L, Bohn A, Bryan CM, Fernández-Velasco DA, Stewart L, Dong M, Huang X, Jin R, Wilson IA, Fuller DH, Baker D.

Nature. 2017 Oct 5;550(7674):74-79. doi: 10.1038/nature23912. Epub 2017 Sep 27.

2.

Global analysis of protein folding using massively parallel design, synthesis, and testing.

Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D.

Science. 2017 Jul 14;357(6347):168-175. doi: 10.1126/science.aan0693.

3.

Accurate de novo design of hyperstable constrained peptides.

Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D.

Nature. 2016 Oct 20;538(7625):329-335. doi: 10.1038/nature19791. Epub 2016 Sep 14.

5.

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

Rocklin GJ, Mobley DL, Dill KA.

J Chem Theory Comput. 2013 Jul 9;9(7):3072-3083.

6.

Blind prediction of charged ligand binding affinities in a model binding site.

Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA.

J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26.

7.

Separated topologies--a method for relative binding free energy calculations using orientational restraints.

Rocklin GJ, Mobley DL, Dill KA.

J Chem Phys. 2013 Feb 28;138(8):085104. doi: 10.1063/1.4792251.

8.

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK.

J Mol Biol. 2009 Dec 11;394(4):747-63. doi: 10.1016/j.jmb.2009.09.049. Epub 2009 Sep 24.

9.

Docking for fragment inhibitors of AmpC beta-lactamase.

Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK.

Proc Natl Acad Sci U S A. 2009 May 5;106(18):7455-60. doi: 10.1073/pnas.0813029106. Epub 2009 Apr 22.

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