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Q-score represents the quality function of Ca-alignment, maximized by the SSM alignment algorithm. Quality of alignment is a complex characteristics, which takes both the alignment length and RMSD into account. In general, more meaningful 3D alignments correspond to lower RMSD and higher number of aligned residues Nalgn. However, it is almost always possible to achieve lower RMSD at the expense of the alignment length and vice versa. Q-score, given by expression
Nalgn*Nalgn
Q = -------------------------
(1+(RMSD/R0)2)*Nres1*Nres2
reduces the effect of RMSD - Nalgn balance on the estimation
of alignments (Nres1 and Nres2 stand for the
number of residues in the aligned proteins, and empirical parameter
R0 is set to 3 Å).
Q-score reaches 1 only in the case of identical structures, and drops down with increasing RMSD or decreasing alignment length. Our practice shows that higher Q-scores indicate "better" (according to the most's intuition) matches far more often then RMSD and alignment length alone.
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