Fig. 2

Binding modes predicted by Vina and DINC for the protein-peptide complex with PDB code 2O9V. The protein receptor is represented by a grey surface in both images. The conformation of the peptide ligand as reported in the 2O9V PDB entry is represented by blue sticks in both images. The best result obtained when redocking this peptide with Vina is represented by yellow sticks in the left-hand side image; the all-atom RMSD between this conformation and the blue one is 5.61 Å. The best result obtained when redocking this peptide with DINC is represented by red sticks in the right-hand side image; the all-atom RMSD between this conformation and the blue one is 1.1 Å; only the ends of the peptide are not well aligned with the crystal structure