Pengyu Ren
Pengyu Ren
Department of Biomedical Engineering, The University of Texas at Austin
Verified email at - Homepage
Cited by
Cited by
Polarizable atomic multipole water model for molecular mechanics simulation
P Ren, JW Ponder
The Journal of Physical Chemistry B 107 (24), 5933-5947, 2003
The COMPASS force field: parameterization and validation for phosphazenes
H Sun, P Ren, JR Fried
Computational and Theoretical Polymer Science 8 (1-2), 229-246, 1998
Current status of the AMOEBA polarizable force field
JW Ponder, C Wu, P Ren, VS Pande, JD Chodera, MJ Schnieders, ...
The journal of physical chemistry B 114 (8), 2549-2564, 2010
Consistent treatment of inter‐and intramolecular polarization in molecular mechanics calculations
P Ren, JW Ponder
Journal of computational chemistry 23 (16), 1497-1506, 2002
Ion solvation thermodynamics from simulation with a polarizable force field
A Grossfield, P Ren, JW Ponder
Journal of the American Chemical Society 125 (50), 15671-15682, 2003
Polarizable atomic multipole-based AMOEBA force field for proteins
Y Shi, Z Xia, J Zhang, R Best, C Wu, JW Ponder, P Ren
Journal of chemical theory and computation 9 (9), 4046-4063, 2013
Polarizable atomic multipole-based molecular mechanics for organic molecules
P Ren, C Wu, JW Ponder
Journal of chemical theory and computation 7 (10), 3143-3161, 2011
Systematic improvement of a classical molecular model of water
LP Wang, T Head-Gordon, JW Ponder, P Ren, JD Chodera, PK Eastman, ...
The Journal of Physical Chemistry B 117 (34), 9956-9972, 2013
Calculation of protein–ligand binding free energy by using a polarizable potential
D Jiao, PA Golubkov, TA Darden, P Ren
Proceedings of the National Academy of Sciences 105 (17), 6290-6295, 2008
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential
D Jiao, C King, A Grossfield, TA Darden, P Ren
The Journal of Physical Chemistry B 110 (37), 18553-18559, 2006
Temperature and pressure dependence of the AMOEBA water model
P Ren, JW Ponder
The Journal of Physical Chemistry B 108 (35), 13427-13437, 2004
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure
JP Piquemal, L Perera, GA Cisneros, P Ren, LG Pedersen, TA Darden
The Journal of chemical physics 125 (5), 054511, 2006
Classical electrostatics for biomolecular simulations
GA Cisneros, M Karttunen, P Ren, C Sagui
Chemical reviews 114 (1), 779-814, 2014
Polarizable molecular dynamics simulation of Zn (II) in water using the AMOEBA force field
JC Wu, JP Piquemal, R Chaudret, P Reinhardt, P Ren
Journal of chemical theory and computation 6 (7), 2059-2070, 2010
Biomolecular electrostatics and solvation: a computational perspective
P Ren, J Chun, DG Thomas, MJ Schnieders, M Marucho, J Zhang, ...
Quarterly reviews of biophysics 45 (4), 427, 2012
Virtual screening using molecular simulations
T Yang, JC Wu, C Yan, Y Wang, R Luo, MB Gonzales, KN Dalby, P Ren
Proteins: Structure, Function, and Bioinformatics 79 (6), 1940-1951, 2011
Automation of AMOEBA polarizable force field parameterization for small molecules
JC Wu, G Chattree, P Ren
Theoretical chemistry accounts 131 (3), 1-11, 2012
Tinker 8: software tools for molecular design
JA Rackers, Z Wang, C Lu, ML Laury, L Lagardère, MJ Schnieders, ...
Journal of chemical theory and computation 14 (10), 5273-5289, 2018
Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
D Jiao, J Zhang, RE Duke, G Li, MJ Schnieders, P Ren
Journal of computational chemistry 30 (11), 1701-1711, 2009
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum
MJ Schnieders, NA Baker, P Ren, JW Ponder
The Journal of chemical physics 126 (12), 03B623, 2007
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