Dataset of "Understanding the Contagiousness of Covid-19 Strains: A Geometric Approach"

Published: 19 September 2023| Version 1 | DOI: 10.17632/t55tp4y9jj.1
Paola Vottero,


Representative snapshots selected from the dominant clusters of the Molecular Dynamics (MD) simulations trajectories of ACE2, antibodies m396 and CR3022, Spike RBD, SARS-CoV-2 main protease, and human hemoglobin (PDB entries 2DD8, 6VW1, 6W41, 2AJF, 6LU7, 6W63, 6Y2E, and 1NQP) as input for the subsequent geometrical analysis. MD simulations were performed with the AMBER16 software after a structure preparation step performed in the Molecular Operating Environment (MOE) software. Each structure was solvated in a cubic box with a 12 Å side length, using a three-point (TIP3P) water model using the AmberTools 16 leap program. To adjust the salt concentration to the physiological value of 0.15 M and neutralize the system, Na+ and Cl− ions were incorporated. The minimization of the complexes was carried out in two steps using the steepest descent (5000 steps) and conjugate gradient (5000 steps) methods consecutively. During the first step, the structure was restrained, and only solvent atoms were minimized. Next, the minimization was performed without restraints, utilizing the same parameters. Following the minimization step, the MD simulations were carried out in three stages: heating, density equilibration, and production. Each solvated system was heated to 298 K for 500 ps in the heating stage, with weak restraints applied to all backbone atoms. Next, using weak restraints, density equilibration was performed for 1 ns at 298 K under constant pressure. The last stage of the MD simulations involved carrying out MD production for a duration of 100 ns without any restraints. The protein trajectory was visually inspected using the VMD package. Clustering analysis was performed on the protein trajectory using Amber's CPPTRAJ program.



University of Alberta


Molecular Dynamics, COVID-19