Rocklin GJ - Search Results

1

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. Rocklin GJ, et al. J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26. J Mol Biol. 2013. PMID: 23896298 Free PMC article.

2

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. Boyce SE, et al. Among authors: rocklin gj. J Mol Biol. 2009 Dec 11;394(4):747-63. doi: 10.1016/j.jmb.2009.09.049. Epub 2009 Sep 24. J Mol Biol. 2009. PMID: 19782087 Free PMC article.

3

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

Rocklin GJ, Mobley DL, Dill KA. Rocklin GJ, et al. J Chem Phys. 2013 Feb 28;138(8):085104. doi: 10.1063/1.4792251. J Chem Phys. 2013. PMID: 23464180 Free PMC article.

4

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Rocklin GJ, et al. J Chem Phys. 2013 Nov 14;139(18):184103. doi: 10.1063/1.4826261. J Chem Phys. 2013. PMID: 24320250 Free PMC article.

5

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

Rocklin GJ, Mobley DL, Dill KA. Rocklin GJ, et al. J Chem Theory Comput. 2013 Jul 9;9(7):3072-3083. doi: 10.1021/ct400315q. J Chem Theory Comput. 2013. PMID: 24015114 Free PMC article.

6

Docking for fragment inhibitors of AmpC beta-lactamase.

Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK. Teotico DG, et al. Among authors: rocklin gj. Proc Natl Acad Sci U S A. 2009 May 5;106(18):7455-60. doi: 10.1073/pnas.0813029106. Epub 2009 Apr 22. Proc Natl Acad Sci U S A. 2009. PMID: 19416920 Free PMC article.

7

Phosphorylation of RhoGDI by Src regulates Rho GTPase binding and cytosol-membrane cycling.

DerMardirossian C, Rocklin G, Seo JY, Bokoch GM. DerMardirossian C, et al. Mol Biol Cell. 2006 Nov;17(11):4760-8. doi: 10.1091/mbc.e06-06-0533. Epub 2006 Aug 30. Mol Biol Cell. 2006. PMID: 16943322 Free PMC article.

8

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. Chevalier A, et al. Among authors: rocklin gj. Nature. 2017 Oct 5;550(7674):74-79. doi: 10.1038/nature23912. Epub 2017 Sep 27. Nature. 2017. PMID: 28953867 Free PMC article.

9

Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.

Peng X, Baxa M, Faruk N, Sachleben JR, Pintscher S, Gagnon IA, Houliston S, Arrowsmith CH, Freed KF, Rocklin GJ, Sosnick TR. Peng X, et al. Among authors: rocklin gj. J Chem Theory Comput. 2022 Jan 11;18(1):550-561. doi: 10.1021/acs.jctc.1c00960. Epub 2021 Dec 22. J Chem Theory Comput. 2022. PMID: 34936354 Free PMC article.

10

Computational design of a synthetic PD-1 agonist.

Bryan CM, Rocklin GJ, Bick MJ, Ford A, Majri-Morrison S, Kroll AV, Miller CJ, Carter L, Goreshnik I, Kang A, DiMaio F, Tarbell KV, Baker D. Bryan CM, et al. Among authors: rocklin gj. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2102164118. doi: 10.1073/pnas.2102164118. Proc Natl Acad Sci U S A. 2021. PMID: 34272285 Free PMC article.

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