Jay W. Ponder

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 8

Top Topics

Emergent Behavior

Complex Systems

Energy Minimization

Top Venues

J. Comput. Chem.

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

Publications

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. J. Chem. Inf. Model. 63 (9) (2023)
Yuanjun Shi, Marie L. Laury, Zhi Wang, Jay W. Ponder
AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. J. Comput. Aided Mol. Des. 35 (1) (2021)
Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Frédéric Célerse, Pengyu Y. 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-GPUs systems. CoRR (2020)
Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Y. Ren, Jean-Philip Piquemal
Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. CoRR (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. J. Comput. Aided Mol. Des. 32 (10) (2018)
Matthew Harger, Daniel Li, Zhi Wang, Kevin N. Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Y. Ren
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J. Comput. Chem. 38 (23) (2017)
Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks
corrections. J. Comput. Aided Mol. Des. 30 (11) (2016)
Christophe Narth, Louis Lagardère, Étienne Polack, Nohad Gresh, Qiantao Wang, David R. Bell, Joshua A. Rackers, Jay W. Ponder, Pengyu Y. Ren, Jean-Philip Piquemal
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J. Comput. Chem. 37 (5) (2016)
Jin Yu Xiang, Jay W. Ponder
A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. J. Comput. Chem. 34 (9) (2013)
Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren
Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. 32 (5) (2011)
Pengyu Y. Ren, Jay W. Ponder
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 23 (16) (2002)
Reece K. Hart, Rohit V. Pappu, Jay W. Ponder
Exploring the similarities between potential smoothing and simulated annealing. J. Comput. Chem. 21 (7) (2000)
Michael J. Dudek, K. Ramnarayan, Jay W. Ponder
Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions. J. Comput. Chem. 19 (5) (1998)
Michael J. Dudek, Jay W. Ponder
Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins. J. Comput. Chem. 16 (7) (1995)