I have docked numerous ligands into my protein of interest, I would like to know how I can calculate the binding affinities between protein and ligands, or alternatively, how can the docking scores be converted to binding affinities?
Thank you in advance!
Perform molecular dynamic studies by schrodinger and calculate free energy and then get binding affinity.
On the basis of docking score not get binding affinity
Docking scores in Schrodinger's Glide are binding affinities (in kcal/mole), though very inaccurate ones. Hence, they don't need conversion. For (slightly) better binding free energy predictions, use Molecular Mechanics Generalized Born Surface Area (MM-GBSA). Or, for significantly more accurate predictions, use FEP+. But you don't have to this with Schrodinger. MM-GBSA (or MM-PBSA) and alchemical FEP simulations can be performed using any standard molecular dynamics software, such as, Gromacs, NAMD, Amber, etc.
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