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2020 – today
- 2023
[j12]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): 2769-2782 (2023)- 2021
- [j11]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): 79-93 (2021) - 2020
- [i2]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 abs/2011.01207 (2020)
2010 – 2019
- 2019
- [i1]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 abs/1906.01211 (2019) - 2018
- [j10]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): 1087-1095 (2018) - 2017
- [j9]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): 2047-2055 (2017) - 2016
- [j8]Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks:
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. J. Comput. Aided Mol. Des. 30(11): 1087-1100 (2016) - [j7]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): 494-506 (2016) - 2013
- [j6]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): 739-749 (2013) - 2011
- [j5]Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren:
Multipole electrostatics in hydration free energy calculations. J. Comput. Chem. 32(5): 967-977 (2011)
2000 – 2009
- 2002
- [j4]Pengyu Y. Ren, Jay W. Ponder:
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 23(16): 1497-1506 (2002) - 2000
- [j3]Reece K. Hart, Rohit V. Pappu, Jay W. Ponder:
Exploring the similarities between potential smoothing and simulated annealing. J. Comput. Chem. 21(7): 531-552 (2000)
1990 – 1999
- 1998
- [j2]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): 548-573 (1998) - 1995
- [j1]Michael J. Dudek, Jay W. Ponder:
Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins. J. Comput. Chem. 16(7): 791-816 (1995)
Coauthor Index
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