Structural Distance Metric (SDM) as defined by Johnson and coworkers ( J Mol Evol. 1990 Jan;30(1):43-59) is

SDM = -100 * LOG (W1*PFTE+W2*SRMS)


PFTE = Number of topologically equivalent residues

Sequence length of the smallest domain

SRMS = 1-(RMSD (in Å)/3.0)

W1 = (1-PFTE+1-SRMS)/2

W2 = (PFTE+SRMS)/2


Structural Distance metric following the work of Levitt and Gerstein ( Proc Natl Acad Sci U S A. 1998 May 26;95(11):5913-5920) is defined as

SDM = -100* (1.0 - S)

Where S = SS-(GP/2)

SS = (1/Nres) * (S1/(1+(dij/3.0)2), dij = distance between topologically equivalent ith and jth C-as and Nres is the number of residue-residue alignment positions.

GP = (Ngap/Nali), Ngap = number of insertions in deletions (this excludes the ones in the N-terminal and C-terminal regions) and Nali = total alignment length (starting from the first residue to residue alignment position to the last residue to residue alignment position).