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Pengyu Ren
Pengyu Ren
Department of Biomedical Engineering, The University of Texas at Austin
Geverifieerd e-mailadres voor mail.utexas.edu - Homepage
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Polarizable atomic multipole water model for molecular mechanics simulation
P Ren, JW Ponder
The Journal of Physical Chemistry B 107 (24), 5933-5947, 2003
16892003
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
16301998
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
15652010
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
7552013
Consistent treatment of inter‐and intramolecular polarization in molecular mechanics calculations
P Ren, JW Ponder
Journal of computational chemistry 23 (16), 1497-1506, 2002
6942002
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
6492003
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
5422018
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
5082011
Polarizable force fields for biomolecular simulations: Recent advances and applications
Z Jing, C Liu, SY Cheng, R Qi, BD Walker, JP Piquemal, P Ren
Annual Review of biophysics 48 (1), 371-394, 2019
3852019
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
3752013
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
3072006
Classical electrostatics for biomolecular simulations
GA Cisneros, M Karttunen, P Ren, C Sagui
Chemical reviews 114 (1), 779-814, 2014
2912014
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
2912008
AMOEBA polarizable atomic multipole force field for nucleic acids
C Zhang, C Lu, Z Jing, C Wu, JP Piquemal, JW Ponder, P Ren
Journal of chemical theory and computation 14 (4), 2084-2108, 2018
2612018
Temperature and pressure dependence of the AMOEBA water model
P Ren, JW Ponder
The Journal of Physical Chemistry B 108 (35), 13427-13437, 2004
2592004
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
L Lagardère, LH Jolly, F Lipparini, F Aviat, B Stamm, ZF Jing, M Harger, ...
Chemical science 9 (4), 956-972, 2018
2392018
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), 2006
2392006
Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis
C Wang, PH Nguyen, K Pham, D Huynh, TBN Le, H Wang, P Ren, R Luo
Journal of computational chemistry 37 (27), 2436-2446, 2016
2322016
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
2252011
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), 427-491, 2012
2232012
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Artikelen 1–20