Figure 6. Comparison of two comparative models analysis methods: filtering by ligand binding pocket residues and clustering on RMSD.

For each receptor, the ten lowest energy models of the largest five clusters are represented in green and the one hundred lowest energy models from the knowledge-based filter on residues in the ligand binding pocket are represented in blue. The width of the beanplot area represents the number of models having a particular A) receptor RMSD and B) pocket residue RMSD, with the corresponding horizontal lines representing the average RMSD for all models clustered by RMSD (green) and models from the knowledge-based filter (blue).