Protein stability and compactness analysis
Root mean square deviation (RMSD) and root mean square fluctuations
(RMSF) were analyzed using the GROMACS[77] in build analysis
modules, gmx rms & gmx rmsf [79]. RMSD was calculated for the
protein backbone atoms and RMSF were calculated for c-alpha atoms. The
radius of gyration and end-to-end distance analysis were also performed
using the inbuilt GROMACS modules like gmx gyrate and gmx polystat
respectively. Also, gmx sasa was used to calculate the total solvent
assessable surface area.