Use case 1: receptor with flexible side chains
In this case we have a receptor we want to dock against (4EK3_rec.pdbqt) and a known ligand for this receptor (4EK4_lig.pdbqt). Both molecules have been prepared for AutoDock4 (i.e. exist in the PDBQT format).
agfr -l 4EK4_lig.pdbqt -r 4EK3_rec.pdbqt -P 7.0 -f A:ILE10,PHE82 -o 4EK3_rec_FR_10_82
More details about running this commands are available here.
The resulting target file 4EK3_rec_FR_10_82.trg file provides a description of a rigid receptor suitable for docking (with AutoDockFR) ligands prepared for AutoDock4 into the binding site of the known ligand. The file can be inspect using the following command:
Here we re-dock a known ligand, that has been randomized (i.e. its conformation as well as it positions and orientation in the crystal structure have been randomly modified). This is a proof-of-concept docking aimed at illustrating the use of adfr and verifying that the docking procedure is able to reproduce a known result.
adfr -l 4EK4_random.pdbqt -t 4EK3_rec_FR_10_82.trg --jobName flexres --nbRuns 8 --maxEvals 20000 -O --seed 1
Details about this calculation are available here.
The file can be inspect using the following command:
Docking Results Object files (.dro) can be opened by Pmv. A group is created containing the ligand and receptor molecules. For docking with flexible side chains, a selection is created for the receptor flexible side chains. Both molecules are displayed and the inter-molecular hydrogen bonds are displayed. If there is more than one solution, the group can be scrolled using the mouse middle button or the arrow keys on the keyboard. The space bar on the keyboards allows toggling on and off an animation flipping between the solutions. The Home and End keys on the keyboard will jump to the first and last solutions respectively.