LigClean FAQ
What do I need to get aligned ligands ready for QUELO or QuValent?
Ligand Preparation takes as input an SDF for the reference ligand with a bound structure and an SDF or SMILES for all additional ligands. No other information is required, though you will get better results if you are confident that the other ligands bind in the same binding site.
Do I get just one aligned structure for each of my ligands?
No, Ligand Preparation generates multiple potential alignments, allowing you to choose the one that makes the most sense for each ligand. You can also automatically pick the conformer with the lowest energy or the one with the greatest overlap to the reference.
I prefer to prepare my ligands with a different program. Can I import the prepared ligands from this program instead of using the Ligand Preparation tool?
Yes. using the QSimulate Ligand Preparation tool is optional. If you have ligands fully prepared, then you can import them directly into QUELO or QuValent.