Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins. - Michael J. Dudek; Jay W. Ponder (J. Comput. Chem., 1995)

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions. - Michael J. Dudek; K. Ramnarayan; Jay W. Ponder (J. Comput. Chem., 1998)

Exploring the similarities between potential smoothing and simulated annealing. - Reece K. Hart; Rohit V. Pappu; Jay W. Ponder (J. Comput. Chem., 2000)

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. - Pengyu Y. Ren; Jay W. Ponder (J. Comput. Chem., 2002)

Multipole electrostatics in hydration free energy calculations. - Yue Shi; Chuanjie Wu; Jay W. Ponder; Pengyu Y. Ren (J. Comput. Chem., 2011)

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. - Jin Yu Xiang; Jay W. Ponder (J. Comput. Chem., 2013)

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. - Frank C. Pickard IV; Gerhard König; Florentina Tofoleanu; Juyong Lee; Andrew C. Simmonett; Yihan Shao; Jay W. Ponder; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2016)

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. - 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 (J. Comput. Chem., 2016)

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. - Matthew Harger; Daniel Li; Zhi Wang 021; Kevin N. Dalby; Louis Lagardère; Jean-Philip Piquemal; Jay W. Ponder; Pengyu Y. Ren (J. Comput. Chem., 2017)

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. - Marie L. Laury; Zhi Wang 021; Aaron S. Gordon; Jay W. Ponder (J. Comput. Aided Mol. Des., 2018)

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. - Luc-Henri Jolly; Alejandro Duran; Louis Lagardère; Jay W. Ponder; Pengyu Y. Ren; Jean-Philip Piquemal (CoRR, 2019)

Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. - Olivier Adjoua; Louis Lagardère; Luc-Henri Jolly; Arnaud Durocher; Thibaut Very; Isabelle Dupays; Zhi Wang 021; Théo Jaffrelot Inizan; Frédéric Célerse; Pengyu Y. Ren; Jay W. Ponder; Jean-Philip Piquemal (CoRR, 2020)

AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. - Yuanjun Shi; Marie L. Laury; Zhi Wang 021; Jay W. Ponder (J. Comput. Aided Mol. Des., 2021)

Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. - Moses K. J. Chung; Ryan J. Miller; Borna Novak; Zhi Wang; Jay W. Ponder (J. Chem. Inf. Model., 2023)