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Journal Articles Scientific Reports Year : 2021

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

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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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Dates and versions

hal-03636461 , version 1 (10-04-2022)

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