Protein - ligand interactions from a quantum ...
Type de document :
Compte-rendu et recension critique d'ouvrage
DOI :
Titre :
Protein - ligand interactions from a quantum fragmentation perspective : the case of the SARS-CoV-2 main protease interacting with α−ketoamide inhibitors
Auteur(s) :
Genovese, Luigi [Auteur]
Laboratory of Atomistic Simulation [LSIM]
Dawson, William [Auteur]
RIKEN Center for Computational Science [Kobe] [RIKEN CCS]
Nakajima, Takahito [Auteur]
RIKEN Center for Computational Science [Kobe] [RIKEN CCS]
Cristiglio, Viviana [Auteur]
Institut Laue-Langevin [ILL]
Vallet, Valérie [Auteur]
Physico-Chimie Moléculaire Théorique [PCMT]
Masella, Michel [Auteur]
Laboratoire de Biologie Structurale et Radiobiologie [LBSR]
Laboratory of Atomistic Simulation [LSIM]
Dawson, William [Auteur]
RIKEN Center for Computational Science [Kobe] [RIKEN CCS]
Nakajima, Takahito [Auteur]
RIKEN Center for Computational Science [Kobe] [RIKEN CCS]
Cristiglio, Viviana [Auteur]
Institut Laue-Langevin [ILL]
Vallet, Valérie [Auteur]
Physico-Chimie Moléculaire Théorique [PCMT]
Masella, Michel [Auteur]
Laboratoire de Biologie Structurale et Radiobiologie [LBSR]
Titre de la revue :
The Journal of Chemical Physics
Pagination :
214121
Éditeur :
American Institute of Physics
Date de publication :
2023-06-07
ISSN :
0021-9606
Discipline(s) HAL :
Chimie/Chimie théorique et/ou physique
Physique [physics]/Physique [physics]/Chimie-Physique [physics.chem-ph]
Physique [physics]/Physique [physics]/Chimie-Physique [physics.chem-ph]
Résumé en anglais : [en]
We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable ...
Lire la suite >We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable Molecular Modeling, MM, approach to perform MD simulations and on an efficient DFT Linear Scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme in particular by checking the ability of MM and DFT to reproduce results from high-end <i>ab initio</i> computations regarding such inhibitors. The DFT approach enables an a posterior fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs.Lire moins >
Lire la suite >We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable Molecular Modeling, MM, approach to perform MD simulations and on an efficient DFT Linear Scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme in particular by checking the ability of MM and DFT to reproduce results from high-end <i>ab initio</i> computations regarding such inhibitors. The DFT approach enables an a posterior fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs.Lire moins >
Langue :
Anglais
Vulgarisation :
Non
Projet ANR :
Source :
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- https://chemrxiv.org/ndownloader/files/24599345
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- microscopic-factors-modulating-the-interactions-between-the-sars-co-v-2-main-protease-and-a-ketoamide-inhibitors.pdf
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- md-Genovese-JCP2023-158-21412.pdf
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