(a)What is RMSD and what is it used for?
(b) Proteins are not rigid, but flexible. How could the RMSD definition be modified to cope with flexibility? Give the advantages and disadvantages of the basic RMSD definition and
(a) RMSD is the root-mean-square deviation of atomic positions. It is the measure of the average distance between the atoms of superimposed proteins. RMSD is used to compare and measure the similarity of the three-dimensional structure of homologous proteins.
(b) As proteins are dynamic structures with fluctuating structures, the RMSD can be modified to as RMSF - root mean square fluctuation. The measuring of the RMSD via spectroscopy or NMR provides the characteristic of the deviation over time giving important physical information concerning the structural similarities of the proteins.