Zobrazeno 1 - 10
of 78
pro vyhledávání: '"Jay W. Ponder"'
Publikováno v:
Journal of Chemical Information and Modeling. 63:2769-2782
Publikováno v:
The Journal of Physical Chemistry B. 126:7579-7594
Polarizability, or the tendency of the electron distribution to distort under an electric field, often depends on the local chemical environment. For example, the polarizability of a chloride ion is larger in gas phase compared to a chloride ion solv
Publikováno v:
J Comput Aided Mol Des
As part of the SAMPL7 host-guest binding challenge, the AMOEBA force field was applied to calculate the absolute binding free energy for 16 charged organic ammonium guests to the TrimerTrip host, a recently reported acyclic cucurbituril-derived clip
Autor:
Léa El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hédin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardère, Jean-Philip Piquemal, Davide Sabbadin
Publikováno v:
Chemical Science
Chemical Science, 2022, ⟨10.1039/D1SC05892D⟩
Chemical Science, 2022, ⟨10.1039/D1SC05892D⟩
We report a fast-track computationally-driven discovery of new SARS-CoV2 Main Protease (Mpro) inhibitors whose potency range from mM for initial non-covalent ligands to high nM for the final covalent compound (IC50=830 +/- 50 nM). The project extensi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a7fb3c770ad5b156560e839423dea37d
https://hal.science/hal-03361062
https://hal.science/hal-03361062
Autor:
Léa, El Khoury, Zhifeng, Jing, Alberto, Cuzzolin, Alessandro, Deplano, Daniele, Loco, Boris, Sattarov, Florent, Hédin, Sebastian, Wendeborn, Chris, Ho, Dina, El Ahdab, Theo, Jaffrelot Inizan, Mattia, Sturlese, Alice, Sosic, Martina, Volpiana, Angela, Lugato, Marco, Barone, Barbara, Gatto, Maria Ludovica, Macchia, Massimo, Bellanda, Roberto, Battistutta, Cristiano, Salata, Ivan, Kondratov, Rustam, Iminov, Andrii, Khairulin, Yaroslav, Mykhalonok, Anton, Pochepko, Volodymyr, Chashka-Ratushnyi, Iaroslava, Kos, Stefano, Moro, Matthieu, Montes, Pengyu, Ren, Jay W, Ponder, Louis, Lagardère, Jean-Philip, Piquemal, Davide, Sabbadin
Publikováno v:
Chemical science. 13(13)
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease (M
Publikováno v:
PLoS ONE, Vol 10, Iss 4, p e0123146 (2015)
Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-reso
Externí odkaz:
https://doaj.org/article/fab67cfb47104468b85d76e19086753d
Publikováno v:
J Chem Theory Comput
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. Thi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::349fcec72eba03b86802c2ce5260c198
http://arxiv.org/abs/2106.13116
http://arxiv.org/abs/2106.13116
Autor:
Thomas L. Casavant, Pengyu Ren, Guowei Qi, Jack R. Lynn, Jean-Philip Piquemal, Louis Lagardère, Andrew C. Thiel, Brandon D. Walker, Michael J. Schnieders, Jay W. Ponder, Rae A. Corrigan
Publikováno v:
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation, American Chemical Society, 2021, ⟨10.1021/acs.jctc.0c01286⟩
Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01286⟩
J Chem Theory Comput
Journal of Chemical Theory and Computation, American Chemical Society, 2021, ⟨10.1021/acs.jctc.0c01286⟩
Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01286⟩
J Chem Theory Comput
Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we descr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0f132e345f72a1656878ffbad801d2e0
https://hal.archives-ouvertes.fr/hal-03183306
https://hal.archives-ouvertes.fr/hal-03183306
Publikováno v:
Journal of Chemical Theory and Computation
Autor:
Louis Lagardère, Alejandro Duran, Pengyu Ren, Jean-Philip Piquemal, Jay W. Ponder, Luc-Henri Jolly
Publikováno v:
Living Journal of Computational Molecular Science
Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩
Living Journal of Computational Molecular Science, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩
Living Journal of Computational Molecular Science, University of Colorado Boulder
Living Journal of Computational Molecular Science, University of Colorado Boulder, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩
Living Journal of Computational Molecular Science, 2019, 1 (2), ⟨10.33011/livecoms.1.2.10409⟩
Living Journal of Computational Molecular Science, University of Colorado Boulder
International audience; This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine pr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eea2b3723d90ebcf5292a9f7bfe4393a
http://arxiv.org/abs/1906.01211
http://arxiv.org/abs/1906.01211