Figure 3

The heat maps depicting binary image representations of the ligand binding pocket shapes for MMP-1. On the left panel, each column represents the conditional bits and each row represents the pocket shape of a given conformer. The bit position is set (red) if the conformer is in contact with the 3D points. The bit positions were clustered using an agglomerative complete linkage method, while the conformers were ordered according to the membership in the accompanying MDS plot. Tyr 240 (green) and Arg 214 (blue), the most influential residues in shaping the pockets, are labeled "240" and "214", respectively, over the bit blocks they are in contact with. For each pocket shape, the number of bits off is counted and plotted in the middle panel. On the right panel, the heat map depicts shape incompatibility between a conformer and a ligand. The columns represent the ligands from the known crystal structures, and their incompatibility with each conformer is coded by red (the darker, the more compatible). For example, the clusters 1~6 could not accommodate any of the known ligands.