Theo dõi
Julie Anne Harris
Julie Anne Harris
Senior Software Engineer, Applied Research Associates
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Tiêu đề
Trích dẫn bởi
Trích dẫn bởi
Năm
Amber 2023
DA Case, HM Aktulga, K Belfon, IY Ben-Shalom, JT Berryman, SR Brozell, ...
University of California, San Francisco, 2023
61312023
Effects of geometry and chemistry on hydrophobic solvation
RC Harris, BM Pettitt
Proceedings of the National Academy of Sciences 111 (41), 14681-14686, 2014
722014
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
622019
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
592018
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
552020
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
532022
From data to probability densities without histograms
BA Berg, RC Harris
Computer Physics Communications 179 (6), 443-448, 2008
522008
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
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
442020
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
422013
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
372010
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
362017
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
352018
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
322013
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
302018
Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
RC Harris, AH Boschitsch, MO Fenley
The Journal of Chemical Physics 140 (7), 2014
292014
Protein collapse driven against solvation free energy without H‐bonds
D Karandur, RC Harris, BM Pettitt
Protein Science 25 (1), 103-110, 2016
282016
Reconciling the understanding of ‘hydrophobicity’with physics-based models of proteins
RC Harris, BM Pettitt
Journal of Physics: Condensed Matter 28 (8), 083003, 2016
262016
Examining the assumptions underlying continuum-solvent models
RC Harris, BM Pettitt
Journal of chemical theory and computation 11 (10), 4593-4600, 2015
242015
Opposites attract: shape and electrostatic complementarity in protein-DNA complexes
RC Harris, T Mackoy, AC Dantas Machado, D Xu, R Rohs, MO Fenley
232012
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