Compare Structure and Sequence Similarity of bNAbs Binding Different gp120 Sites

The purpose of this interface is to ease the structure comparisons of bNAbs and bound antigens and to facilitate the understanding the role of structure in biological properties of broadly neutralizing antibodies. User first selects which Env antigenic site he or she wants to explore. CD4bs antigenic site is shown by default when you open the tool. Change the binding site by selecting it from the drop down menu and click “Submit”. The page displays three pairs of heatmaps. Two upper pairs of heatmaps provide links to POSA comparisons of bNAbs H and L chains. The last pair of heatmaps is for bound antigens (where available). The left heatmap presents color coded structural-similarity of PDB chains, the right map presents sequence similarity of the respective chains. Please continue reading below.



Binding SiteChain type

The left heatmap presents color coded structural-similarity of PDB chains (in RMSD, color coded from blue for small RMSD (minimum = 0 Angstroms) to red for large RMSD (maximum value = 6 A). The right map presents sequence similarity of the respective chains (% identity, starting at 40% (low similarity, colored red) to 100% (high similarity, colored blue). Moving the cursor over any heatmap and clicking on the particular square (for example, 3se9H - 4jamH) leads to protein structure and sequence alignment for the respective structures and simplifies access to POSA comparison of antibody/antigen chains. Comparisons between left and right matrices emphasize interesting cases when, for example, a good sequence similarity corresponds to a poor structure similarity or vice versa. Comparisons of heatmaps between H, L and antigen chains facilitate identifying of bNAbs and antigens that has unusual structure or unique binding mode (Ab-Ag interaction).



An alternative interface to bNAbs structure comparisons is available here.