Figure 3.
Distribution of RMSD and Ne values of the TOPOFIT alignments for structurally related proteins. The alignments were calculated for proteins representing different structural classes against the test set of 2905 proteins (see Materials and Methods). All the TOPOFIT alignments show RMSD better than 2 Å. The distribution also shows three distinct areas of the structural neighbors, which are circled by the dashed ellipses: A, exact match; B, structural subfamily; and C, structural superfamily.