Published May 17, 2022
| Version 1
Dataset
Open
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
Authors/Creators
- 1. University of California Irvine
Description
This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spike protein as well as for four different variants (alpha, beta, kappa and delta). The simulations of the RBD only system are propagated for 300 ns and for the RBD-Antibody complex for 500 ns. The trajectories are saved at 100 ps interval. The Steered MD simulation trajectories (WT_RBD_B38_SMD_1.dcd etc.) and collective variables files are also included (WT_RBD_B38_SMD_1.colvars.traj etc.). There are 5 SMD trajectories for each RBD antibody pair. The details of the simulation can be obtained from the preprint: https://doi.org/10.1101/2021.08.13.456317
Notes
Funding: NSF MCB 2028443
Computing Resources: University of California Irvine HPC3, San Diego Supercomputer Center
Files
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