(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.

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.<br>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.<br>Note: The refined crystal structure of the protease of our partner Prof. Yang group from ShanghaiTech is oficially released: https://www.rcsb.org/structure/6LU7<br><br>Part 1 of 5:XHD_LC1a<br>XHD_LC1b+ images of the 3 docked starting positions<br>

本数据集包含上海科技大学杨教授课题组针对新型冠状病毒2019-nCoV主蛋白酶（Mpro）与配体洛匹那韦（lopinavir）形成的复合物的未精修晶体结构开展的分子动力学模拟（Molecular Dynamics, MD）实验，模拟条件为310开尔文下运行500皮秒，详情见下文注释。配体（LP1、LP2、LP3）的初始构象源自分子对接实验。文件名后缀(a、b、c)代表使用随机初始速度开展的同一场分子动力学模拟的重复实验组。
该存档文件中还包含一张表征蛋白-配体接触频率的热图，热图中以绿色框标注的区域对应模拟过程中发生氢键相互作用的情况。
注释：上海科技大学杨教授课题组合作团队解析的该蛋白酶的精修晶体结构已正式发布：https://www.rcsb.org/structure/6LU7

第1部分（共5部分）：XHD_LC1a
XHD_LC1b 及3种对接初始构象的图像