Hocky GM - Search Results

1

Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.

Sasmal S, Pal T, Hocky GM, McCullagh M. Sasmal S, et al. Among authors: hocky gm. J Chem Theory Comput. 2024 May 14;20(9):3492-3502. doi: 10.1021/acs.jctc.4c00223. Epub 2024 Apr 25. J Chem Theory Comput. 2024. PMID: 38662196 Free PMC article.

2

Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories.

Klem H, Hocky GM, McCullagh M. Klem H, et al. Among authors: hocky gm. J Chem Theory Comput. 2022 May 10;18(5):3218-3230. doi: 10.1021/acs.jctc.1c01290. Epub 2022 Apr 28. J Chem Theory Comput. 2022. PMID: 35483073 Free PMC article.

3

Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.

Sasmal S, McCullagh M, Hocky GM. Sasmal S, et al. Among authors: hocky gm. J Chem Theory Comput. 2023 Jul 25;19(14):4427-4435. doi: 10.1021/acs.jctc.3c00051. Epub 2023 May 2. J Chem Theory Comput. 2023. PMID: 37130367 Free PMC article.

4

Residue-Level Allostery Propagates through the Effective Coarse-Grained Hessian.

Lake PT, Davidson RB, Klem H, Hocky GM, McCullagh M. Lake PT, et al. Among authors: hocky gm. J Chem Theory Comput. 2020 May 12;16(5):3385-3395. doi: 10.1021/acs.jctc.9b01149. Epub 2020 Apr 17. J Chem Theory Comput. 2020. PMID: 32251581

5

Assessment of chemistry knowledge in large language models that generate code.

White AD, Hocky GM, Gandhi HA, Ansari M, Cox S, Wellawatte GP, Sasmal S, Yang Z, Liu K, Singh Y, Peña Ccoa WJ. White AD, et al. Among authors: hocky gm. Digit Discov. 2023 Jan 26;2(2):368-376. doi: 10.1039/d2dd00087c. eCollection 2023 Apr 11. Digit Discov. 2023. PMID: 37065678 Free PMC article.

6

Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water.

Calio PB, Hocky GM, Voth GA. Calio PB, et al. Among authors: hocky gm. J Chem Theory Comput. 2020 Sep 8;16(9):5675-5684. doi: 10.1021/acs.jctc.0c00558. Epub 2020 Aug 13. J Chem Theory Comput. 2020. PMID: 32786913

7

Coarse-Grained Directed Simulation.

Hocky GM, Dannenhoffer-Lafage T, Voth GA. Hocky GM, et al. J Chem Theory Comput. 2017 Sep 12;13(9):4593-4603. doi: 10.1021/acs.jctc.7b00690. Epub 2017 Aug 31. J Chem Theory Comput. 2017. PMID: 28800392 Free PMC article.

8

Computing equilibrium free energies through a nonequilibrium quench.

Liu K, Rotskoff GM, Vanden-Eijnden E, Hocky GM. Liu K, et al. Among authors: hocky gm. J Chem Phys. 2024 Jan 21;160(3):034109. doi: 10.1063/5.0176700. J Chem Phys. 2024. PMID: 38240301

9

Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.

Dama JF, Hocky GM, Sun R, Voth GA. Dama JF, et al. Among authors: hocky gm. J Chem Theory Comput. 2015 Dec 8;11(12):5638-50. doi: 10.1021/acs.jctc.5b00907. Epub 2015 Nov 20. J Chem Theory Comput. 2015. PMID: 26587809 Free PMC article.

10

Assessing models of force-dependent unbinding rates via infrequent metadynamics.

Peña Ccoa WJ, Hocky GM. Peña Ccoa WJ, et al. Among authors: hocky gm. J Chem Phys. 2022 Mar 28;156(12):125102. doi: 10.1063/5.0081078. J Chem Phys. 2022. PMID: 35364872 Free PMC article.

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