Figure 2
System stability and root mean square fluctuation (RMSF) analysis of FMDV-SAT1 capsid subunits (VP1–VP4).
(a) Root mean square division per residue (RMSDres) in FMDV-SAT1 capsid calculated from 50 ns simulations. Residue stability increases from blue to red. (b) Energy stability (top plot) and Root mean square division, RMSD, (bottom plot) of the system throughout the 50 ns simulation time. (c) Root mean square fluctuation of residues (RMSF) of FMDV-SAT1 capsid viral particles (VP1–VP4) throughout the 50 ns simulation time. Identified residues that are involved in cavities in FMDV-SAT1 capsid viral particles (VP1–VP4) using ten structure-based analysis tools were illustrated using green vertical lines. GROMACS package was used for simulations and trajectory analysis while VMD44 and R45 package were used for the representation of the molecule and drawing the plots respectively.
