I have to validate one of my docking protocol but I haven't a co-crystalized ligand. There is a way to validate it? Thanks in advance.
Using different score functions
One way to validate the docking results is scoring your poses using a different score function. You will need to use one of this two methods:
- Use another docking software: in this case you have to do a score-in-place procedure, i.e. not re-docking your ligands, just score the poses. For example, if you work with GLIDE (that is the software that do the docking in the Schrodinger suite, not MAESTRO), you can use AUTODOCK-VINA, PLANTS, GOLD, etc.
- Use scoring software: these software have the only purpose to score the poses using score functions obtained from experimental data. Examples are XSCORE, AGL-SCORE, DLSCORE, etc.
If you obtain the same pose rank using a different score functions, then your docking results are good (without any bias due to the software used)