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Table 1 Secondary Structure Matching (SSM) parameters

From: Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction

Query

PDB code

RMSD (Ã…)

Q-score

Z-score

PFF0015c_3

2of3

1.07

0.657

10

PFL2660w_5

2f31

3.54

0.190

1.7

  1. Root mean square deviation (RMSD) is calculated between the C-alpha atoms of the matched residues in the best 3D superimposition of the query and target structures. The percentage of identity (%ID) is the number of identical amino acids in the structural alignment (%ID is not given in table). Q-score is the ratio between RMSD and the number of aligned amino acids and is considered as a measure of quality of alignment (for identical structure Q = 1). Z-score provides the statistical significance of a fold match in terms of standard Gaussian statistics, the higher Z-score; the higher is the significance of the match