Jay W Ponder

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 23

Top Venues

Journal of chemical theory and computation

The Journal of chemical physics

Chemical science

Journal of computer-aided molecular design

Washington University in Saint Louis

Harvard University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Washington University in Saint Louis Jul 01 2015

United States

Professor :: Chemistry, Biomedical Engineering, Biochemistry & Molecular Biophysics

Education History

Harvard University Sep 01 1978 - Nov 01 1984

United States

PHD

Publications

Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Andrew C Thiel, Matthew J Speranza, Sanika Jadhav, Lewis L Stevens, Daniel K Unruh, Pengyu Ren, Jay W Ponder, Jana Shen, Michael J Schnieders
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 20 (7) (2024)
Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. The Journal of chemical physics 161 (1) (2024)
Rae A Corrigan, Andrew C Thiel, Jack R Lynn, Thomas L Casavant, Pengyu Ren, Jay W Ponder, Michael J Schnieders
A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. The Journal of chemical physics 159 (5) (2023)
Moses K J Chung, Ryan J Miller, Borna Novak, Zhi Wang, Jay W Ponder
Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. Journal of chemical information and modeling (2023)
Léa El Khoury, Zhifeng F Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hédin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W Ponder, Louis Lagardère, Jean-Philip Piquemal, Davide Sabbadin
Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation. Chemical science 13 (13) (2022)
Moses K J Chung, Zhi Wang, Joshua A Rackers, Jay W Ponder
Classical Exchange Polarization: An Anisotropic Variable Polarizability Model. The journal of physical chemistry. B 126 (39) (2022)
Rae A Corrigan, Guowei Qi, Andrew C Thiel, Jack R Lynn, Brandon D Walker, Thomas L Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W Ponder, Pengyu Ren, Michael J Schnieders
Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of chemical theory and computation 17 (4) (2021)
Joshua A Rackers, Roseane R Silva, Zhi Wang, Jay W Ponder
Polarizable Water Potential Derived from a Model Electron Density. Journal of chemical theory and computation 17 (11) (2021)
Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Fréderic Célerse, Pengyu Ren, Jay W Ponder, Jean-Philip Piquemal
Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems. Journal of chemical theory and computation 17 (4) (2021)
Yuanjun Shi, Marie L Laury, Zhi Wang, Jay W Ponder
AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. Journal of computer-aided molecular design 35 (1) (2020)
Joshua A Rackers, Jay W Ponder
Classical Pauli repulsion: An anisotropic, atomic multipole model. The Journal of chemical physics 150 (8) (2019)
Marie L Laury, Zhi Wang, Aaron S Gordon, Jay W Ponder
Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. Journal of computer-aided molecular design 32 (10) (2018)
Joshua A Rackers, Zhi Wang, Chao Lu, Marie L Laury, Louis Lagardère, Michael J Schnieders, Jean-Philip Piquemal, Pengyu Ren, Jay W Ponder
Tinker 8: Software Tools for Molecular Design. Journal of chemical theory and computation 14 (10) (2018)
Joshua A Rackers, Qiantao Wang, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren, Jay W Ponder
An optimized charge penetration model for use with the AMOEBA force field. Physical chemistry chemical physics : PCCP 19 (1) (2018)
Joshua A Rackers, Chengwen Liu, Pengyu Ren, Jay W Ponder
A physically grounded damped dispersion model with particle mesh Ewald summation. The Journal of chemical physics 149 (8) (2018)
Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, Zhifeng F Jing, Matthew Harger, Hedieh Torabifard, Gerardo Andrés Cisneros, Michael J Schnieders, Nohad Gresh, Yvon Maday, Pengyu Y Ren, Jay W Ponder, Jean-Philip Piquemal
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical science 9 (4) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jay W Ponder