Fig. 7.
(A) Incremental neighborhood optimization strategy used in the design of octasaccharide sequences. Five hexasaccharide sequences that were found to be most optimal from each of the two libraries (UANRE and GlcNNRE) were selected and then 38 disaccharide sequences of UANRE and GlcNNRE libraries were appended at either the reducing or the non-reducing ends. The total of 5 × 38 × 4 = 760 octasaccharide sequences were then studied using the dual-filter CVLS protocol. (B) Ten octasaccharide sequences from the GlcNNRE library and six sequences from the UANRE library satisfied the CVLS dual-filter criteria. Helices A (hA), D (hD) and P (hP) of antithrombin are shown in ribbon form and residues Arg132, Arg129, Lys125 and Arg114 are shown in ball and stick display. The crystal structure of DEFGH in green ball and sticks display is shown to highlight correspondence with the CVLS predicted poses.