Jay W. Ponder

发表

Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Zhi Wang, Jean-Philip Piquemal, Kevin N. Dalby, 2017, J. Comput. Chem..

Accurate modeling of the intramolecular electrostatic energy of proteins

Jay W. Ponder, Michael J. Dudek, J. Ponder, 1995, J. Comput. Chem..

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

Jay W. Ponder, Michael J. Dudek, K. Ramnarayan, 1998, J. Comput. Chem..

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field

Zhi Wang, Jay W. Ponder, Marie L. Laury, 2018, Journal of Computer-Aided Molecular Design.

Exploring the similarities between potential smoothing and simulated annealing

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 2000, J. Comput. Chem..

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0] pdf

Jean-Philip Piquemal, Alejandro Duran, Louis Lagardère, 2019, ArXiv.

Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]

Jean-Philip Piquemal, Alejandro Duran, Jay W. Ponder, 2019, Living Journal of Computational Molecular Science.

Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems

Jean-Philip Piquemal, Zhi Wang, Jay W. Ponder, 2020, ArXiv.

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles

Nohad Gresh, Jean-Philip Piquemal, Qiantao Wang, 2016, J. Comput. Chem..

Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 1998 .

Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations

Pengyu Y. Ren, Jay W. Ponder, Pengyu Y. Ren, 2002, J. Comput. Chem..

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

Jay W. Ponder, Jin Yu Xiang, J. Ponder, 2013, J. Comput. Chem..

Tinker 8: Software Tools for Molecular Design.

Jean-Philip Piquemal, Zhi Wang, Louis Lagardère, 2018, Journal of chemical theory and computation.

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKa corrections

Bernard R. Brooks, Juyong Lee, Gerhard König, 2016, Journal of Computer-Aided Molecular Design.

Systematic Improvement on the Classical Molecular Model of Water

Vijay S. Pande, John D. Chodera, Jay W. Ponder, 2014 .

Multipole electrostatics in hydration free energy calculations

Yue Shi, Pengyu Y. Ren, Jay W. Ponder, 2011, J. Comput. Chem..

Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization

Jay W. Ponder, Craig E. Kundrot, Frederic M. Richards, 1991 .

A potential smoothing algorithm accurately predicts transmembrane helix packing

Garland R. Marshall, Jay W. Ponder, Rohit V. Pappu, 1999, Nature Structural Biology.

Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization

Frank Jensen, Jay W. Ponder, Pengyu Ren, 2007 .

Stereochemistry of the hygrolidins

Jay W. Ponder, J. Ponder, E. Corey, 1984 .

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, 2018, Journal of chemical theory and computation.

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

Nohad Gresh, Jean-Philip Piquemal, Jay W. Ponder, 2015, Journal of chemical theory and computation.

Tertiary Templates for Proteins Use of Packing Criteria in the Enumeration of Allowed Different Structural Classes Sequences

Jay W. Ponder, Frederic M. Richards, J. Ponder, 1987 .

Exploring the similarities between potential smoothing and simulated annealing

Jay W. Ponder, Rohit V. Pappu, Reece K. Hart, 2000 .