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Hai Nguyen
Hai Nguyen
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Cited by
Cited by
Year
AMBER 2017
DA Case, DS Cerutti, TE Cheatham, III, TA Darden, RE Duke, TJ Giese, ...
University of California, San Francisco, 2017
5513*2017
Improved generalized born solvent model parameters for protein simulations
H Nguyen, DR Roe, C Simmerling
Journal of chemical theory and computation 9 (4), 2020-2034, 2013
4762013
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent
H Nguyen, J Maier, H Huang, V Perrone, C Simmerling
Journal of the American Chemical Society 136 (40), 13959-13962, 2014
2402014
AmberTools
DA Case, HM Aktulga, K Belfon, DS Cerutti, GA Cisneros, VWD Cruzeiro, ...
Journal of chemical information and modeling 63 (20), 6183-6191, 2023
2132023
NGLview–interactive molecular graphics for Jupyter notebooks
H Nguyen, DA Case, AS Rose
Bioinformatics 34 (7), 1241-1242, 2018
1412018
AmberTools 16
DA Case, RM Betz, W Botello-Smith, DS Cerutti, TE Cheatham III, ...
University of California, San Francisco, 2016
1222016
Refinement of generalized born implicit solvation parameters for nucleic acids and their complexes with proteins
H Nguyen, A Perez, S Bermeo, C Simmerling
Journal of chemical theory and computation 11 (8), 3714-3728, 2015
662015
AMBER 2016
RE Duke, TJ Giese, H Gohlke, AW Goetz, N Homeyer, S Izadi, P Janowski, ...
University of California, San Francisco 1 (3), 2016
612016
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix
NW Moriarty, PA Janowski, JM Swails, H Nguyen, JS Richardson, ...
Acta Crystallographica Section D: Structural Biology 76 (1), 51-62, 2020
292020
ParmEd
J Swails, C Hernandez, DL Mobley, H Nguyen, LP Wang, P Janowski
URL: https://github. com/ParmEd/ParmEd, 2010
252010
Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation
AB Rubenstein, K Blacklock, H Nguyen, DA Case, SD Khare
Journal of chemical theory and computation 14 (11), 6015-6025, 2018
232018
Improving the description of salt bridge strength and geometry in a Generalized Born model
Y Shang, H Nguyen, L Wickstrom, A Okur, C Simmerling
Journal of Molecular Graphics and Modelling 29 (5), 676-684, 2011
202011
AMBER 2015
DA Case, JT Berryman, RM Betz, DS Cerutti, . T.E. Cheatham, III, ...
University of California, San Francisco, 2015
3*2015
PYTRAJ v1.0.0.dev1: Interactive data analysis for molecular dynamics simulations.
H Nguyen, DR Roe, J Swails, DA Case
http://dx.doi.org/10.5281/zenodo.44612, 2016
2*2016
A Pareto-optimal approach for protein structure evaluation using Amber and Rosetta energy functions.
A Rubenstein, K Blacklock, H Nguyen, D Case, S Khare
2017
AMBER 2016
DA Case, RM Betz, W Botello-Smith, DS Cerutti, TE Cheatham, III, ...
University of California, San Francisco, 2016
2016
AMBER 15
University of California, San Francisco, 2015
2015
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Articles 1–17