Scalable Hybrid Deep Neural Networks/Polarizable Potentials Biomolecular Simulations including Long-range Effects

Autor: Théo Jaffrelot Inizan, Thomas Plé, Olivier Adjoua, Pengyu Ren, Hatice Gökcan, Olexandr Isayev, Louis Lagardère, Jean-Philip Piquemal

Publikováno v: Chemical Science
Chemical Science, 2023, ⟨10.1039/D2SC04815A⟩

International audience; Deep-HP is a scalable extension of the Tinker-HP multi-GPUs molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Networks (DNNs) models. Deep-HP increases DNNs MD capabilities by orders of magnitu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e3204c37f45afbf96b891d166d560cc0
https://hal.science/hal-03738403

Actin-AMOEBA

Autor: Adrien Schahl, Louis Lagardère, Brandon Walker, Pengyu Ren, Antoine Jégou, Matthieu Chavent, Jean-Philip Piquemal

Depository gathering all the relevant data for the work published in the following preprint: β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions (https://doi.org/10.1101/2022.12.16.520803) Th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::809a176c76b81c0345155cdd56aa039b

Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory

Autor: Pier Paolo Poier, Olivier Adjoua, Louis Lagardère, Jean-Philip Piquemal

Publikováno v: Journal of Physical Chemistry Letters
Journal of Physical Chemistry Letters, 2023, pp.1609-1617. ⟨10.1021/acs.jpclett.2c03722⟩

International audience; We extend our recently proposed Deep Learning-aided many-body dispersion (DNN-MBD) model to quadrupole polarizability (Q) terms using a generalized Random Phase Approximation (RPA) formalism enabling to include van der Waals c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cb1658f9c758dce95a07393482dd4d82
http://arxiv.org/abs/2210.09784

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

Autor: Krystel El Hage, Giovanni Ribaudo, Louis Lagardère, Alberto Ongaro, Philippe H. Kahn, Luc Demange, Jean-Philip Piquemal, Giuseppe Zagotto, Nohad Gresh

Publikováno v: Journal of Chemical Information and Modeling
Journal of Chemical Information and Modeling, 2022, 62 (24), pp.6649-6666. ⟨10.1021/acs.jcim.2c00337⟩

International audience; GC-rich sequences are recurring motifs in oncogenes and retroviruses, and could be targeted by non-covalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligop

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e906c9d976aa0d537451c2b4ce24a327
https://hal.science/hal-03624169

Computationally driven discovery of targeting SARS-CoV-2 Mpro inhibitors: from design to experimental validation

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⟩

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