%0 Generic %A Cespugli, Marco %A Durmaz, Vedat %A Steinkellner, Georg %A Gruber, Christian C. %D 2020 %T 6 molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with different conformations of lopinavir. %U https://figshare.com/articles/dataset/6_molecular_dynamics_simulations_of_coronavirus_2019-nCoV_protease_model_in_complex_with_different_conformations_of_lopinavir_/11764158 %R 10.6084/m9.figshare.11764158.v2 %2 https://ndownloader.figshare.com/files/21448587 %2 https://ndownloader.figshare.com/files/21448647 %2 https://ndownloader.figshare.com/files/21448701 %2 https://ndownloader.figshare.com/files/21448776 %2 https://ndownloader.figshare.com/files/21448803 %2 https://ndownloader.figshare.com/files/21448860 %2 https://ndownloader.figshare.com/files/21448866 %2 https://ndownloader.figshare.com/files/21448869 %2 https://ndownloader.figshare.com/files/21448998 %2 https://ndownloader.figshare.com/files/21449028 %K ncov %K virus %K protease %K Mpro %K molecular dynamics %K lopinavir %K Bioinformatics %K Virology %X 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.
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