Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly - Molecular Dynamics Simulation Dataset

<p>The molecular dynamics (MD) simulation dataset. The contents:</p> <ul> <li><strong>5ire_BIOMT_expanded.pdb</strong>: The complete biological assembly of the&nbsp;cryo-EM structure of Zika Virus (PDB ID:5IRE)&nbsp;</li> <li><strong>5ire_Mprotein_BIOMT_expanded.pdb</strong>:&nbsp;The M proteins extracted from the complete biological assembly of the&nbsp;cryo-EM structure of Zika Virus (PDB ID:5IRE).&nbsp; The biological assembly shows the dimeric organization of M proteins.</li> <li><strong>0chol.zip, 10chol.zip, 20chol.zip, and 30chol.zip</strong> contain&nbsp;simulation input and output files for the simulated membrane compositions: 0:100, 10:90, 20:80, 30:70 (mol%:mol%) Cholesterol:POPC, respectively.&nbsp; <ul> <li>In each zip file, there are 5 directories: <strong>wt,&nbsp;R253L+F257A,&nbsp;R253L+F257S, K275L+Y278A,&nbsp;K275L+Y278S</strong>&nbsp;corresponding to each simulated&nbsp;M protein dimer variant: wild type, CARC 2-A, CARC 2-S, CARC 3-A, and CARC 3-S.&nbsp;In each directory, there are the following files: <ul> <li><strong>toppar</strong>: This directory contains all force field topologies and parameters</li> <li><strong>topol.top</strong>: GROMACS&nbsp;topology (top) file</li> <li><strong>index.ndx</strong>: GROMACS index (ndx) file</li> <li><strong>prod.mdp</strong>: GROMACS MD&nbsp;parameters (mdp)&nbsp; file</li> <li><strong>0, 1, 2, 3, 4, 5, 6, 7, 8, 9</strong>: These directories contain the simulation&nbsp;inputs and outputs for each simulation&nbsp;repeat. In each of these directories, there are the following files:&nbsp; <ul> <li><strong>t0.pdb</strong>: The pdb file of the starting&nbsp;coordinates</li> <li><strong>prod0.tpr</strong>: GROMACS binary run input (tpr) file&nbsp;</li> <li><strong>prod0.edr</strong>: GROMACS energy (edr) file</li> <li><strong>prod0.gro</strong>: GROMACS output coordinates and velocities after&nbsp;1 microsecond of simulation</li> <li><strong>prod0.cpt</strong>: GROMACS checkpoint file&nbsp;after 1 microsecond of simulation</li> <li><strong>noW.pdb</strong>: The pdb file of the starting&nbsp;coordinates with all water molecules removed</li> <li><strong>noW.xtc</strong>:&nbsp; GROMACS compressed trajectory (xtc)&nbsp;file with all water molecules removed</li> </ul> </li> </ul> </li> </ul> </li> </ul>