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Article Dans Une Revue Journal of Chemical Physics Année : 2023

Protein - ligand interactions from a quantum fragmentation perspective : the case of the SARS-CoV-2 main protease interacting with α−ketoamide inhibitors

Résumé

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 ab initio 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.

Dates et versions

hal-02933298 , version 1 (08-09-2020)

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Citer

Luigi Genovese, William Dawson, Takahito Nakajima, Viviana Cristiglio, Valérie Vallet, et al.. Protein - ligand interactions from a quantum fragmentation perspective : the case of the SARS-CoV-2 main protease interacting with α−ketoamide inhibitors. Journal of Chemical Physics, 2023, 158 (21), pp.214121. ⟨10.1063/5.0148064⟩. ⟨hal-02933298⟩
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