Figure 4

An example of a library of 78 fragments generated by the program. The picture to the left shows the target receptor with its ligand, and the one to the right shows the target receptor with the fragments generated. The target receptor is the protein-ligand complex with PDB code “2br6”, and the dataset used to perform the pocket similarity search is the refined set of PDBbind (v 2008) which contains 1401 complexes. The following parameters were used: Water molecules are removed; AD distance cutoff 5.8 Å with an epsilon value 0.01 Å; size we used for an acceptable sub-graph match is 8 atoms; maximum RMSD cutoff used is 0.1 Å; and the safety distance used to avoid a collision is 1.95 Å.