Jay W. Ponder - RankMe

14 papers Journal 14

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. J. Chem. Inf. Model. Moses K. J. Chung, Ryan J. Miller, Borna Novak, Zhi Wang, Jay W. Ponder
2021	J	`jnl`	AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge. J. Comput. Aided Mol. Des. Yuanjun Shi, Marie L. Laury, Zhi Wang, Jay W. Ponder
2020	J	`jnl`	Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems. CoRR 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
2019	J	`jnl`	Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel's HPC Architectures: a Living Review [Article v1.0]. CoRR Luc-Henri Jolly, Alejandro Duran, Louis Lagardère, Jay W. Ponder, Pengyu Y. Ren, Jean-Philip Piquemal
2018	J	`jnl`	Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. J. Comput. Aided Mol. Des. Marie L. Laury, Zhi Wang, Aaron S. Gordon, Jay W. Ponder
2017	J	`jnl`	Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J. Comput. Chem. Matthew Harger, Daniel Li, Zhi Wang, Kevin N. Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Y. Ren
2016	J	`jnl`	Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p J. Comput. Aided Mol. Des. Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks
2016	J	`jnl`	Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J. Comput. Chem. 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
2013	J	`jnl`	A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field. J. Comput. Chem. Jin Yu Xiang, Jay W. Ponder
2011	J	`jnl`	Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren
2002	J	`jnl`	Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. Pengyu Y. Ren, Jay W. Ponder
2000	J	`jnl`	Exploring the similarities between potential smoothing and simulated annealing. J. Comput. Chem. Reece K. Hart, Rohit V. Pappu, Jay W. Ponder
1998	J	`jnl`	Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions. J. Comput. Chem. Michael J. Dudek, K. Ramnarayan, Jay W. Ponder
1995	J	`jnl`	Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins. J. Comput. Chem. Michael J. Dudek, Jay W. Ponder