Fig. 9.

Alignments of the ligand surfaces found by MS3ALIGN and not SURFCOMP for the thermolysin inhibitor dataset. The aligning portions of the surface are shown as opaque and the rest is shown with transparency. A stick representation of the ligands is also shown. a The best three alignments of the 4TMN’s 0PK ligand (light pink) with 5TLN’s BAN ligand (green) aligns the two aromatic rings of 0PK with those of BAN. b The best two results of 6TMN’s 0PJ ligand (dark blue) with the 5TLN’s BAN(green) show alignment of aromatic rings from both ligands