InnoCoVprotease_Lopinavir_hbonds.pse (13.83 MB)View fileThis item contains files with download restrictions
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PyMOL presentation showing the H-bond network established during 6 molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with different conformations of lopinavir. Textual list of the interactions included.
This PyMOL presentation contains PDB structures representing the
centroids of the MD simulations with 6 conformaers on comparative model
of novel coronavirus 2019-nCoV protease Mpro produced by Innophore. In
each structure, the ligand lopinavir is displayed with the indication of
the hydrogen bond network established throughout the simulation (300 ps
/ 310 K = 36.85°C). Note: The dashed lines reported in the said
structures do not necessarily reflect the presence of a hydrogen bond in
the particular frame displayed (the "centroid" of the simulation), but
indicate that the bonds occurred at least once during the simulation. Point
clouds generated by the Catalophore platform are represented in sphere
mode and their color is function of the buriedness index. Point clouds
were calculated on the whole active site of the enzyme disregarding the
presence of a ligand. A textual list of the H-bond interactions is included.