Inspecting docking results
A docking result consists of a ligand binding mode and the connected docking score. No matter if the docking result is found in a Docking Results Table or in a Molecule Project, there is easy access to both aspects of the result.
Docking score and other data
In a Docking Results Table, each entry represents a docking result, and the docking score is found in the column with the title "Score". From the table Side Panel, columns are accessible that show how the score can be broken down into the contributions described in The docking algorithms. In the table you can also find a column listing how many flexible bonds each ligand have. The conformation of the ligand is changed in the docking simulation, through rotations around the ligand flexible bonds. Furthermore, the number of flexible bonds in a molecule is related to the ligand entropy loss on binding. If the "Calculate RMSDs between input structure and results" is selected in the Dock Ligands wizard, the Docking Results Table will also contain a column with RMSD values. Please note that the RMSD values are only relevant for ligands that are docked into their initial position, as is the case for the docking of a co-crystallized ligand.
In a Molecule Project, the docking score and number of flexible bonds are displayed in the Side Panel Property viewer, when the docking result is selected in the Project Tree.
Ligand binding mode
In a Molecule Project, a docking result entry can be displayed together with the protein and other molecules in the project, to visualize the binding mode of the ligand in the binding site. To visualize the ligand interaction in atomic detail, select the relevant docking result entry in the Project Tree and invoke the right-click context menu. From the menu, pick Binding Site Interactions. If this option is not found in the menu, click the Setup Binding Site button below the Project Tree and define the binding site. There are two options for showing binding site interactions; Show Hydrogen Bonds and Create Interacting Atoms Group. Use the Show Hydrogen Bonds option to display protein residues forming hydrogen bonds to the ligand (in wireframe), with the hydrogen bonds shown as blue dashed lines. The hydrogen bonds can be hidden again invoking the context menu on the docking result and selecting Binding Site Interactions | Hide Hydrogen Bonds. Use the Create Interacting Atoms Group option to generate a custom atom group consisting of protein residues and molecules, which have at least one heavy atom within 5 Å of a ligand heavy atom. The atom group appears in the Atom groups category in the Project Tree, and can be hidden using the check box next to it, and the visualization changed using the quick-style buttons found at the bottom of the Project Tree.
In a Docking Results Table, connect to a 3D view using the Select View action in the table Side Panel. Select either the "Embedded molecule project" if available, to see the ligand binding modes in a read-only version of the Molecule Project used as input for the docking, or select an open Molecule Project, where the binding site setup is present. See Viewing Molecule Table structures in 3D for a description of how to see hydrogen bonds and nearby atoms for ligands "visiting" a Molecule Project from a table.