MD simulations of SARS-CoV-2 Spike Protein under static electric fields

This dataset contains trajectories corresponding to all-atom MD simulations of segments of the SARS-CoV-2 Spike Protein, and in-silico mutations, under the influence of moderate external electric fields. The final structures of some of the simulations were used to perform in-silico docking with ACE2 receptor to evaluate the effect of comformational changes (docking was perform with PyDOCK). The file trajectories_6vsb_dt1ns.zip contains trajectories of simulations that were performed on a segment of the Protein Data Bank ID 6VSB comprising RBD, SD1 and SD2. The file trajectories_6m0j_dt1ns.zip correspond to the RBD in Protein Data Bank ID 6M0J. The file trajectories_in-silico_mutations_dt1ns.zip correspond to simulations performed on in-silico generated mutations following the mutations corresponding to WHO Variants of Concern UK, South Africa and Brazil. In all cases, simulations were performed at different electric field intensities ranging between 10⁴ V/m and 10⁷ V/m, with an extra short simulation under very high intensity (10⁹ V/m). The file docked_structures_6m0j.zip contains the 100 best scored docked structures for each case as the output of PyDOCK. Trajectories are stored in GROMACS compressed trajectory file format (.xtc), downsampled to a 1ns timestep. Individual trajectories length are between 300 nanoseconds and 1 microsecond. In-silico docked structures are in PDB format. See linked preprint for more details.本数据集包含SARS-CoV-2刺突蛋白片段的全原子分子动力学（all-atom MD）模拟轨迹，以及中等强度外电场作用下的虚拟突变（in-silico mutation）样本。部分模拟的最终结构被用于与血管紧张素转换酶2（ACE2）开展虚拟分子对接（in-silico docking）实验，以评估构象变化的影响（对接实验通过PyDOCK工具完成）。 文件trajectories_6vsb_dt1ns.zip包含针对蛋白质数据库（Protein Data Bank, PDB）编号6VSB的一段包含受体结合域（Receptor Binding Domain, RBD）、SD1与SD2结构域的蛋白片段所开展的模拟轨迹。文件trajectories_6m0j_dt1ns.zip对应蛋白质数据库编号6M0J中的RBD结构域的模拟轨迹。文件trajectories_in-silico_mutations_dt1ns.zip对应针对遵循世界卫生组织（WHO）关注变异株英国、南非及巴西株突变位点生成的虚拟突变体所开展的模拟轨迹。 所有模拟均在强度介于10⁴ V/m至10⁷ V/m的外电场下开展，另有一组短时模拟使用了极高强度（10⁹ V/m）的外电场。 文件docked_structures_6m0j.zip包含PyDOCK输出的、各实验组得分排名前100的对接后结构。 轨迹文件采用GROMACS压缩轨迹格式（.xtc）存储，并被下采样至1纳秒（nanosecond, ns）的时间步长。单条轨迹的时长介于300纳秒至1微秒（microsecond, μs）之间。 虚拟对接得到的结构采用PDB格式存储。更多细节请参阅关联的预印本。