Molecular dynamics dataset of apo TMPRSS2
Description
This dataset contains all-atom molecular dynamics trajectories of TMPRSS2 (apo). The data was generated with openMM 7.4.0 with the CHARMM36 force field in the NPT ensemble at 310 K. Details about the molecular dynamics setup are given in Hempel, T.; Raich, L.; Olsson, S.; Azouz, N. P.; Klingler, A. M.; Hoffmann, M.; Pöhlmann, S.; Rothenberg, M. E.; Noé, F. Molecular Mechanism of Inhibiting the SARS-CoV-2 Cell Entry Facilitator TMPRSS2 with Camostat and Nafamostat. Chem. Sci. 2021, 10.1039.D0SC05064D. https://doi.org/10.1039/D0SC05064D.
The data was downsampled to a timestep of 1 ns and consists of three parts:
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1TMP_crystal7MEQpruned: Seeded from crystal structure PBD-ID 7MEQ, only catalytic chain. 80 µs cumulative simulation time.
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1TMP_crystal7MEQ: Seeded from crystal structure PBD-ID 7MEQ. Both chains. 77 µs cumulative simulation time.
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1TMP_homology3W94: Seeded from a homology model [S. Rensi et al., 2020, chemRxiv, DOI: 10.26434/ chemrxiv.12009582.]. 534 µs cumulative simulation time.