Root mean square deviation RMSd

RMSd is the standard magnitude to calibrate the deviation of a structure with respect to a reference conformation. It is computed as:

$RMSd=\sqrt{\frac{\sum_i\left(R_i-R_i^0\right)^2}{N}}$

(1),

Where the sum extends for the total number of atoms/residues considered in the calculation ( $N$ ) and the position vectors of the considered structure ( $R_i$ ) and reference conformation ( $R_i^0$ ) are computed after alignment of the structure to the reference conformation to minimize the value of the RMSd. FlexServ uses the Kabsch algorithm (Kabsch, 1976) for alignment of the structures.