Hardy D - Search Results

1

Computer modeling in biotechnology: a partner in development.

Aksimentiev A, Brunner R, Cohen J, Comer J, Cruz-Chu E, Hardy D, Rajan A, Shih A, Sigalov G, Yin Y, Schulten K. Aksimentiev A, et al. Among authors: hardy d. Methods Mol Biol. 2008;474:181-234. doi: 10.1007/978-1-59745-480-3_11. Methods Mol Biol. 2008. PMID: 19031067 Review.

2

Accelerating molecular modeling applications with graphics processors.

Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K. Stone JE, et al. J Comput Chem. 2007 Dec;28(16):2618-40. doi: 10.1002/jcc.20829. J Comput Chem. 2007. PMID: 17894371

3

GPU-accelerated molecular modeling coming of age.

Stone JE, Hardy DJ, Ufimtsev IS, Schulten K. Stone JE, et al. J Mol Graph Model. 2010 Sep;29(2):116-25. doi: 10.1016/j.jmgm.2010.06.010. Epub 2010 Jul 8. J Mol Graph Model. 2010. PMID: 20675161 Free PMC article.

4

Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units.

Hardy DJ, Stone JE, Schulten K. Hardy DJ, et al. Parallel Comput. 2009 Mar 1;35(3):164-177. doi: 10.1016/j.parco.2008.12.005. Parallel Comput. 2009. PMID: 20161132 Free PMC article.

5

Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases.

Le L, Lee EH, Hardy DJ, Truong TN, Schulten K. Le L, et al. PLoS Comput Biol. 2010 Sep 23;6(9):e1000939. doi: 10.1371/journal.pcbi.1000939. PLoS Comput Biol. 2010. PMID: 20885781 Free PMC article.

6

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.

Jiang W, Hardy DJ, Phillips JC, Mackerell AD Jr, Schulten K, Roux B. Jiang W, et al. Among authors: hardy dj. J Phys Chem Lett. 2011;2(2):87-92. doi: 10.1021/jz101461d. J Phys Chem Lett. 2011. PMID: 21572567 Free PMC article.

7

Multilevel summation method for electrostatic force evaluation.

Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. Hardy DJ, et al. J Chem Theory Comput. 2015 Feb 10;11(2):766-79. doi: 10.1021/ct5009075. J Chem Theory Comput. 2015. PMID: 25691833 Free PMC article.

8

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

Hardy DJ, Wolff MA, Xia J, Schulten K, Skeel RD. Hardy DJ, et al. J Chem Phys. 2016 Mar 21;144(11):114112. doi: 10.1063/1.4943868. J Chem Phys. 2016. PMID: 27004867 Free PMC article.

9

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kalé LV, Schulten K, Chipot C, Tajkhorshid E. Phillips JC, et al. Among authors: hardy dj. J Chem Phys. 2020 Jul 28;153(4):044130. doi: 10.1063/5.0014475. J Chem Phys. 2020. PMID: 32752662 Free PMC article.

10

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.

Chen H, Maia JDC, Radak BK, Hardy DJ, Cai W, Chipot C, Tajkhorshid E. Chen H, et al. Among authors: hardy dj. J Chem Inf Model. 2020 Nov 23;60(11):5301-5307. doi: 10.1021/acs.jcim.0c00745. Epub 2020 Sep 1. J Chem Inf Model. 2020. PMID: 32805108 Free PMC article.

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