I have an enzyme with an active site. I want to bind a specific ligand to the site and calculate the Kd value in Maestro or any other program. Also is it possible to mutate the interacting residues of enzyme with ligand and then calculate Kd value or energetic of each mutation involve.
Maestro has a paid module called Glide that can dock a ligand to any site (including active site) of a target protein (enzyme). There are several other free alternatives such as AutoDock, Vina etc. You can do mutation on Maestro (using the build feature) as well as in other programs such as PyMOL.
Dissociation constant (Kd) is a bulk property. However, you can directly get binding energy (formation energy) of two molecules from interatomic potentials (force fields). Now, assuming this formation energy is equivalent to Gibbs energy, you can approximate the dissociation constant using the Gibbs free energy isotherm (ΔG = -RTlnKeq). All the programs (including Maestro) give binding energy; some (such as AutoDock4 but not Vina) reports Kd as well.
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