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Jay Ponder
Jay Ponder
Department of Chemistry, Washington University
Adresse e-mail validée de dasher.wustl.edu - Page d'accueil
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Force fields for protein simulations
JW Ponder, DA Case
Advances in protein chemistry 66, 27-85, 2003
24892003
Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes
JW Ponder, FM Richards
Journal of molecular biology 193 (4), 775-791, 1987
20041987
Polarizable atomic multipole water model for molecular mechanics simulation
P Ren, JW Ponder
The Journal of Physical Chemistry B 107 (24), 5933-5947, 2003
16502003
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
14642010
An efficient newton‐like method for molecular mechanics energy minimization of large molecules
JW Ponder, FM Richards
Journal of computational chemistry 8 (7), 1016-1024, 1987
10931987
TINKER: Software tools for molecular design
JW Ponder
Washington University School of Medicine, Saint Louis, MO 3, 116, 2004
8162004
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
7042013
Consistent treatment of inter‐and intramolecular polarization in molecular mechanics calculations
P Ren, JW Ponder
Journal of computational chemistry 23 (16), 1497-1506, 2002
6822002
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
6352003
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
5142018
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
4912011
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
3612013
Analysis and application of potential energy smoothing and search methods for global optimization
RV Pappu, RK Hart, JW Ponder
The Journal of Physical Chemistry B 102 (48), 9725-9742, 1998
3131998
Accurate modeling of the intramolecular electrostatic energy of proteins
MJ Dudek, JW Ponder
Journal of Computational Chemistry 16 (7), 791-816, 1995
2881995
Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization
CE Kundrot, JW Ponder, FM Richards
Journal of computational chemistry 12 (3), 402-409, 1991
2581991
Temperature and pressure dependence of the AMOEBA water model
P Ren, JW Ponder
The Journal of Physical Chemistry B 108 (35), 13427-13437, 2004
2512004
Revised parameters for the AMOEBA polarizable atomic multipole water model
ML Laury, LP Wang, VS Pande, T Head-Gordon, JW Ponder
The Journal of Physical Chemistry B 119 (29), 9423-9437, 2015
2362015
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
2322018
Light-activated rhodopsin induces structural binding motif in G protein α subunit
OG Kisselev, J Kao, JW Ponder, YC Fann, N Gautam, GR Marshall
Proceedings of the National Academy of Sciences 95 (8), 4270-4275, 1998
2201998
Definition of a metal-dependent/Li (+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure.
JD York, JW Ponder, PW Majerus
Proceedings of the National Academy of Sciences 92 (11), 5149-5153, 1995
2181995
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