Fig. 3

CABS-dock predictions for the 3d1e complex. The image shows CABS-dock 3d1e predictions in two docking modes: default mode (left column, without using any information about the binding interface) and contact information mode (right column, using information about a single side-chain contact). The upper panels show sets of 10,000 models. The middle panels show sets of 1000 top scored models. The lower panel shows sets of 10 top scored models obtained in both docking modes. Peptide models obtained in default and contact information mode are colored in orange and cyan, respectively. The peptide model with the lowest RMSD (from the contact information mode) is shown in green, the peptide from the experimental complex in magenta, and the receptor residue belonging to the side-chain contact used in the docking is marked in red. Ligand-RMSD between this model and the experimental peptide structure is 1.76 Å