Figure 2
From: SABERTOOTH: protein structural alignment based on a vectorial structure representation
Aligned Structural Profiles for Alignment Example 'd1cd9b2' vs. 'd1bpv__'. Figure 2a shows the optimal profile alignment of the ASTRAL [33] domains 'd1cd9b2' and 'd1bpv__' as computed by the first step of SABERTOOTH without refinement. Gaps, as marked by small negative values, are inserted in regions with low connectivities, continuous patterns of larger connectivities are correctly aligned. Figure 2b shows the result for the same example as output by the full SABERTOOTH algorithm including refinement. Comparison to the result of the profile alignment shows only slight corrections introduced by the refinement routine while the overall similarity match is retained. The number of residues close in space after optimal rotation increases from 56 to 78 residues, PSIprofile = 56.6% increases to PSIrefined = 78.8%. Improvement of the alignment is achieved by introducing obvious deviations from the overlap maximization of the structural profiles which implies that some local properties of the structures are not represented in the profiles, as expected by their construction. Three-dimensional superposition for this alignment is shown in Fig. 3.