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6 molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with different conformations of lopinavir.

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posted on 2020-01-29, 18:39 authored by Marco Cespugli, Vedat Durmaz, Georg Steinkellner, Christian C. GruberChristian C. Gruber
Molecular dynamics simulations of comparative model of novel coronavirus 2019-nCoV protease Mpro in complex with 6 different conformations based on the Catalophore point-cloud alignment and (re)- docking of lopinavir into the 2019ncov virus protease model. The docking experiment produced 8 clusters of possible conformations, we chose 6 out of 8 conformers and ran an all-atom 300 ps MD at 310 K (=36.85°C).

-The two images in the main folder refers to the docked structures before MD simulation.
-The file all_centroids.pse contains the frames representing the centroid of the subsequent MD simulation for each docking cluster.
-Each archive contains the centroid in PDB format, the starting frame of the simulation in GRO format and the compressed trajectory in XTC format. In the directory "other_files" there are other data generated during the simulation, i.e. heatmap representing the contact frequency between the ligand atoms and the ones belonging to the homology model.