title: (PART 1 OF 5) 9 molecular dynamics simulations (500ps 3 x 3 replicates) of coronavirus 2019-nCoV protease unrefined crystal structure in complex with 3 different conformations of lopinavir.
author: Marco Cespugli
description: Molecular dynamics simulations (500 ps MD at 310 K) of the unrefined crystal structure by Prof. Yang group from ShanghaiTech of novel coronavirus 2019-nCoV protease Mpro in complex with the ligand lopinavir (see note below). The starting positions of the ligand (LP1, LP2, LP3) derive from docking experiments.The suffixes (a, b, c) on the filenames represent the replicates of the same MD simulation using random initial velocities.The archives contain also an heatmap representing the protein-ligand contact frequencies. Green-boxed occurrences in the heatmap represent hydrogen bond occurrences during the simulation.Note: The refined crystal structure of the protease of our partner Prof. Yang group from ShanghaiTech is oficially released: https://www.rcsb.org/structure/6LU7Part 1 of 5:XHD_LC1aXHD_LC1b+ images of the 3 docked starting positions