Jay Ponder
Jay Ponder
Department of Chemistry, Washington University
Adresse e-mail validée de dasher.wustl.edu - Page d'accueil
TitreCitée parAnnée
Force fields for protein simulations
JW Ponder, DA Case
Advances in protein chemistry 66, 27-85, 2003
18472003
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
17921987
Polarizable atomic multipole water model for molecular mechanics simulation
P Ren, JW Ponder
The Journal of Physical Chemistry B 107 (24), 5933-5947, 2003
12912003
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
9621987
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
9062010
TINKER: Software tools for molecular design
JW Ponder
Version, 2004
6922004
Consistent treatment of inter‐and intramolecular polarization in molecular mechanics calculations
P Ren, JW Ponder
Journal of computational chemistry 23 (16), 1497-1506, 2002
5882002
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
4982003
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
3812013
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
3132011
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
2931998
Accurate modeling of the intramolecular electrostatic energy of proteins
MJ Dudek, JW Ponder
Journal of Computational Chemistry 16 (7), 791-816, 1995
2651995
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
2371991
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
2322013
Temperature and pressure dependence of the AMOEBA water model
P Ren, JW Ponder
The Journal of Physical Chemistry B 108 (35), 13427-13437, 2004
2082004
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
2081998
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
1901995
TINKER, Software Tools for Molecular Design, Version 4.2
JW Ponder
Washington University School of Medicine, St. Louis, 2004
1682004
Tinker, version 4.2
JW Ponder
Tinker Software Tools for Molecular Design, 2004
1572004
The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm
ME Hodsdon, JW Ponder, DP Cistola
Journal of molecular biology 264 (3), 585-602, 1996
1481996
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