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Flexibility and mobility of SARS-CoV-2-related protein structures

Abstract : Abstract The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein—using its complete homo-trimer configuration with 2905 residues—our method identifies a large-scale opening and closing of the S1 subunit through movement of the S $${}^\text{B}$$ B domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.
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https://hal-cnrs.archives-ouvertes.fr/hal-03636461
Contributor : Rudo Roemer Connect in order to contact the contributor
Submitted on : Sunday, April 10, 2022 - 2:37:21 PM
Last modification on : Friday, August 5, 2022 - 2:46:00 PM
Long-term archiving on: : Monday, July 11, 2022 - 6:06:36 PM

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2020.07.12.199364v1.full.pdf
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Rudolf Römer, Navodya Römer, A. Katrine Wallis. Flexibility and mobility of SARS-CoV-2-related protein structures. Scientific Reports, Nature Publishing Group, 2021, 11 (1), pp.4257. ⟨10.1038/s41598-021-82849-2⟩. ⟨hal-03636461⟩

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