Jay W. Ponder

Washington University in St. Louis — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

44h-index15.8kcitations106works3.92yr avg
OpenAlex↗ORCID↗Google Scholar↗Lab page↗

Accepting Students?

No reports yet. Know if this professor is taking students?

Research Topics

Protein Structure and Dynamics(45), Spectroscopy and Quantum Chemical Studies(34), Advanced Chemical Physics Studies(24), DNA and Nucleic Acid Chemistry(19), Enzyme Structure and Function(17)

Publications106 total

Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors
Communications Biology·2025· 2 citedOpen Access
Chain Formation and Addition Drive the Debye Relaxation of Methanol
The Journal of Physical Chemistry B·2025Open Access
Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors
2024· 2 citedOpen Access
Targeting RNA with Small Molecules using State-of-the-Art Methods Provides Highly Predictive Affinities of Riboswitch Inhibitors
2024· 2 citedOpen Access
A new method to calculate broadband dielectric spectra of solvents from molecular dynamics simulations demonstrated with polarizable force fields
The Journal of Chemical Physics·2024· 7 citedOpen Access
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
The Journal of Chemical Physics·2024Open Access
Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of <b>p</b> orbitals
The Journal of Chemical Physics·2024· 3 citedOpen Access
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field
Journal of Chemical Theory and Computation·2024· 15 citedOpen Access
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field
2023· 1 citedOpen Access
A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model
The Journal of Chemical Physics·2023· 4 citedOpen Access
A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model
2023Open Access
A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model
2023Open Access
Accurate Host–Guest Binding Free Energies Using the AMOEBA Polarizable Force Field
Journal of Chemical Information and Modeling·2023· 18 citedOpen Access
Binding free energies from the polarizable AMOEBA force field
Biophysical Journal·2023Open Access
Classical Exchange Polarization: An Anisotropic Variable Polarizability Model
The Journal of Physical Chemistry B·2022· 15 citedOpen Access
Computationally driven discovery of SARS-CoV-2 M<sup>pro</sup>inhibitors: from design to experimental validation
Chemical Science·2022· 39 citedOpen Access
Polarizable Water Potential Derived from a Model Electron Density
Journal of Chemical Theory and Computation·2021· 2 citedOpen Access
Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation (preprint)
arXiv (Cornell University)·2021· 1 citedOpen Access
Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
Journal of Chemical Theory and Computation·2021· 18 citedOpen Access
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·2021· 88 citedOpen Access
page 1 of 6Next →

Frequent Co-authors

Pengyu Ren(22), Jean‐Philip Piquemal(9), Louis Lagardère(7), Michael J. Schnieders(6), Chuanjie Wu(5), Teresa Head‐Gordon(5), Vijay S. Pande(4), Joshua A. Rackers(4), Zhi Wang(4), Zhifeng Jing(4), Rohit V. Pappu(4), Frederic M. Richards(3), Martin Head‐Gordon(3), Chao Lü(3), Marie L. Laury(3), Lee‐Ping Wang(3), Garland R. Marshall(3), Qiantao Wang(3), E. J. Corey(3), David A. Case(2)