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Julie Anne Harris
Julie Anne Harris
Manager of Product Development, ComputChem
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Cited by
Cited by
Year
Amber 2021
DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ...
University of California, San Francisco, 2021
53272021
Effects of geometry and chemistry on hydrophobic solvation
RC Harris, BM Pettitt
Proceedings of the National Academy of Sciences 111 (41), 14681-14686, 2014
702014
GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations
RC Harris, J Shen
Journal of chemical information and modeling 59 (11), 4821-4832, 2019
512019
Generalized Born based continuous constant pH molecular dynamics in Amber: Implementation, benchmarking and analysis
Y Huang, RC Harris, J Shen
Journal of chemical information and modeling 58 (7), 1372-1383, 2018
492018
Comparing the Predictions of the Nonlinear Poisson− Boltzmann Equation and the Ion Size-Modified Poisson− Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an …
ARJ Silalahi, AH Boschitsch, RC Harris, MO Fenley
Journal of chemical theory and computation 6 (12), 3631-3639, 2010
482010
From data to probability densities without histograms
BA Berg, RC Harris
Computer Physics Communications 179 (6), 443-448, 2008
482008
Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors
JA Henderson, N Verma, RC Harris, R Liu, J Shen
The Journal of chemical physics 153 (11), 2020
452020
Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation
RC Harris, AH Boschitsch, MO Fenley
Journal of chemical theory and computation 9 (8), 3677-3685, 2013
392013
Predicting reactive cysteines with implicit-solvent-based continuous constant pH molecular dynamics in amber
RC Harris, R Liu, J Shen
Journal of chemical theory and computation 16 (6), 3689-3698, 2020
372020
Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach
MO Fenley, RC Harris, B Jayaram, AH Boschitsch
Biophysical journal 99 (3), 879-886, 2010
352010
Proton-coupled conformational allostery modulates the inhibitor selectivity for β-secretase
RC Harris, CC Tsai, CR Ellis, J Shen
The journal of physical chemistry letters 8 (19), 4832-4837, 2017
342017
Solvation free energies of alanine peptides: the effect of flexibility
H Kokubo, RC Harris, D Asthagiri, BM Pettitt
The Journal of Physical Chemistry B 117 (51), 16428-16435, 2013
312013
Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
RC Harris, AH Boschitsch, MO Fenley
The Journal of Chemical Physics 140 (7), 2014
302014
How ligand protonation state controls water in protein–ligand binding
JA Henderson, RC Harris, CC Tsai, J Shen
The journal of physical chemistry letters 9 (18), 5440-5444, 2018
272018
Accuracy comparison of generalized Born models in the calculation of electrostatic binding free energies
S Izadi, RC Harris, MO Fenley, AV Onufriev
Journal of chemical theory and computation 14 (3), 1656-1670, 2018
272018
Protein collapse driven against solvation free energy without H‐bonds
D Karandur, RC Harris, BM Pettitt
Protein Science 25 (1), 103-110, 2016
262016
GPU-accelerated all-atom particle-mesh Ewald continuous constant pH molecular dynamics in Amber
JA Harris, R Liu, V Martins de Oliveira, EA Vázquez-Montelongo, ...
Journal of chemical theory and computation 18 (12), 7510-7527, 2022
252022
Reconciling the understanding of ‘hydrophobicity’with physics-based models of proteins
RC Harris, BM Pettitt
Journal of Physics: Condensed Matter 28 (8), 083003, 2016
242016
Examining the assumptions underlying continuum-solvent models
RC Harris, BM Pettitt
Journal of chemical theory and computation 11 (10), 4593-4600, 2015
222015
Opposites attract: shape and electrostatic complementarity in protein-DNA complexes
RC Harris, T Mackoy, AC Dantas Machado, D Xu, R Rohs, MO Fenley
222012
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