FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
Figure 3
Ligand binding pose prediction for human fibroblast collagenase (PDB-ID: 1hfc).
Predicted poses (thick, solid) from FINDSITELHM: (left) superimposed ligand with the anchor portion colored in white, (middle) minimized conformation with Amber and (right) generated by AutoDock are compared to the experimental binding pose of hydroxamate inhibitor (thin, transparent). RMSD values were calculated for heavy atoms. Selected binding residues are shown.