Sokolova A. V.
Small angle scattering laboratory, Institute of Crystallography RAS
Leninskij pr. 59, 119333, Moscow, Russia
Bragg Institute, Australian Nuclear Science and Technology Organization
New Illawarra Road, Lucas Heights, 2234, NSW, Australia
DaRa contains mostly non-homologious structures but obviously there are a lot of similar proteins are left behind. DaRa understands structural similarity in terms of value of so called NSD (normalized spacial discrepancy).
NSD is measure of dissimilarity between the aligned structures and is computed as follows. For every point in the first model, the minimum value among the distances between this point and all points in the second model is found, and the same is done for the points in the second model. These distances are added and normalized against the average distances between the neighboring points for the two models so that the value NSD less then one indicates that the two models are similar. To be confident we are using NSD equals to 0.77 as a threshold. NSD values used for DaRa were calculated using program SupComb.
The current program takes pdb-file name and returns a list of similar structures and corresponding values of NSD between adressed proteins and similar ones.