Can I perform a rigid ligand docking using GOLD?
Although GOLD was designed to dock flexible ligands into protein binding sites, it is possible to perform a rigid ligand docking. To enable this option, go to the Ligand Flexibility option under Global Options in the GOLD Setup interface. Upon activating the "Fix Ligand Rotatable Bonds" tick box, you are presented with three options:
- fix all: use this option to fix all rotatable bonds (i.e. carry out a rigid docking)
- fix all but terminal: use this option to fix all non-terminal rotatable bonds (i.e. not -CH3, -OH, etc.)
- fix specific: use this option to fix user-defined bonds. Hit the Specify Bonds button, then use the Add button to select the atoms involved in the bond(s) to be fixed.