AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
A) A cross-section of the AutoDock carbon affinity map. B) The same cross-section after processing the map to create a gradient inside the protein. Besides creating a potential gradient inside the receptor, this processing also removes the local minima inside the receptor volume. The color gradient outside the protein surface indicates favorable interactions going from weak (green) to strong (blue). Inside the protein surface the color gradient indicates unfavorable interactions going from low (yellow) to highly unfavorable (red).