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J

Jay W. Ponder

Department of Chemistry

44H指数
107论文数
1.6W被引数
收录论文 46
发表时间
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Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors采用最先进的方法使用小分子靶向RNA，能够获得核糖开关抑制剂的预测性极高的亲和力。
errCommunications Biology
IF5.1
err2025-10-01
err0
errOAAI
errNarjes Ansari; Chengwen Liu; Florent Hédin; Jérôme Hénin; Jay W. Ponder; Pengyu Ren; Jean-Philip Piquemal; Louis Lagardère; Krystel El Hage
err分享
err收藏
A new method to calculate broadband dielectric spectra of solvents from molecular dynamics simulations demonstrated with polarizable force fields
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2024-08-12
err2
PREAI
errBone, Rebecca A.; Chung, Moses K. J.; Ponder, Jay W.; Riccardi, Demian; Muzny, Chris; Sundararaman, Ravishankar; Schwarz, Kathleen
err分享
err收藏
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2024-07-03
err0
errOAAI
errGogal, Rose A.; Nessler, Aaron J.; Thiel, Andrew C.; Bernabe, Hernan V.; Corrigan Grove, Rae A.; Cousineau, Leah M.; Litman, Jacob M.; Miller, Jacob M.; Qi, Guowei; Speranza, Matthew J.; Tollefson, Mallory R.; Fenn, Timothy D.; Michaelson, Jacob J.; Okada, Okimasa; Piquemal, Jean-Philip; Ponder, Jay W.; Shen, Jana; Smith, Richard J. H.; Yang, Wei; Ren, Pengyu; Schnieders, Michael J.
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Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2024-05-07
err1
errOAAI
errChung, Moses K. J.; Ponder, Jay W.
err分享
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Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-03-20
err5
errOAAI
errThiel, Andrew C.; Speranza, Matthew J.; Jadhav, Sanika; Stevens, Lewis L.; Unruh, Daniel K.; Ren, Pengyu; Ponder, Jay W.; Shen, Jana; Schnieders, Michael J.
err分享
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A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-08-01
err2
errOAAI
errCorrigan, Rae A.; Thiel, Andrew C.; Lynn, Jack R.; Casavant, Thomas L.; Ren, Pengyu; Ponder, Jay W.; Schnieders, Michael J.
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Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-04-19
err11
PREAI
errChung, Moses K. J.; Miller, Ryan J.; Novak, Borna; Wang, Zhi; Ponder, Jay W.
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Computationally driven discovery of SARS-CoV-2 Mpro inhibitors: from design to experimental validation
errCHEMICAL SCIENCE
IF7.4
err2022-01-01
err20
errOAAI
errEl Khoury, Lea; Jing, Zhifeng; Cuzzolin, Alberto; Deplano, Alessandro; Loco, Daniele; Sattarov, Boris; Hedin, Florent; Wendeborn, Sebastian; Ho, Chris; El Ahdab, Dina; Inizan, Theo Jaffrelot; Sturlese, Mattia; Sosic, Alice; Volpiana, Martina; Lugato, Angela; Barone, Marco; Gatto, Barbara; Macchia, Maria Ludovica; Bellanda, Massimo; Battistutta, Roberto; Salata, Cristiano; Kondratov, Ivan; Iminov, Rustam; Khairulin, Andrii; Mykhalonok, Yaroslav; Pochepko, Anton; Chashka-Ratushnyi, Volodymyr; Kos, Iaroslava; Moro, Stefano; Montes, Matthieu; Ren, Pengyu; Ponder, Jay W.; Lagardere, Louis; Piquemal, Jean-Philip; Sabbadin, Davide
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Polarizable Water Potential Derived from a Model Electron Density
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2021-10-26
err44
errOAAI
errRackers, Joshua A.; Silva, Roseane R.; Wang, Zhi; Ponder, Jay W.
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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2021-03-26
err15
errOAAI
errCorrigan, Rae A.; Qi, Guowei; Thiel, Andrew C.; Lynn, Jack R.; Walker, Brandon D.; Casavant, Thomas L.; Lagardere, Louis; Piquemal, Jean-Philip; Ponder, Jay W.; Ren, Pengyu; Schnieders, Michael J.
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err收藏
Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2021-03-23
err53
errOAAI
errAdjoua, Olivier; Lagardere, Louis; Jolly, Luc-Henri; Durocher, Arnaud; Very, Thibaut; Dupays, Isabelle; Wang, Zhi; Inizan, Theo Jaffrelot; Celerse, Frederic; Ren, Pengyu; Ponder, Jay W.; Piquemal, Jean-Philip
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A structural basis for lithium and substrate binding of an inositide phosphatase
errJOURNAL OF BIOLOGICAL CHEMISTRY
IF3.9
err2021-01-01
err6
errOAAI
errDollins, D. Eric; Xiong, Jian-Ping; Endo-Streeter, Stuart; Anderson, David E.; Bansal, Vinay S.; Ponder, Jay W.; Ren, Yi; York, John D.
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AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge
errJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
IF3.1
err2020-11-03
err24
errOAAI
errShi, Yuanjun; Laury, Marie L.; Wang, Zhi; Ponder, Jay W.
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Classical Pauli repulsion: An anisotropic, atomic multipole model
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2019-02-22
err75
errOAAI
errRackers, Joshua A.; Ponder, Jay W.
err分享
err收藏
Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field
errJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
IF3.1
err2018-10-15
err29
errOAAI
errLaury, Marie L.; Wang, Zhi; Gordon, Aaron S.; Ponder, Jay W.
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err收藏
Tinker 8: Software Tools for Molecular Design
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2018-09-03
err413
errOAAI
errRackers, Joshua A.; Wang, Zhi; Lu, Chao; Laury, Marie L.; Lagardere, Louis; Schnieders, Michael J.; Piquemal, Jean-Philip; Ren, Pengyu; Ponder, Jay W.
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A physically grounded damped dispersion model with particle mesh Ewald summation
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2018-08-31
err21
errOAAI
errRackers, Joshua A.; Liu, Chengwen; Ren, Pengyu; Ponder, Jay W.
err分享
err收藏
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2018-02-13
err215
errOAAI
errZhang, Changsheng; Lu, Chao; Jing, Zhifeng; Wu, Chuanjie; Piquemal, Jean-Philip; Ponder, Jay W.; Ren, Pengyu
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err收藏
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
errCHEMICAL SCIENCE
IF7.4
err2018-01-01
err183
errOAAI
errLagardere, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Felix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, G. Andres; Schnieders, Michael J.; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y.; Ponder, Jay W.; Piquemal, Jean-Philip
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Tinker-OpenMM: Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs
errJOURNAL OF COMPUTATIONAL CHEMISTRY
IF4.8
err2017-06-10
err100
errOAAI
errHarger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardere, Louis; Piquemal, Jean-Philip; Ponder, Jay; Ren, Pengyu
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err收藏

研究方向

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