I’m almost done with a 62 million ligands screen and I want to do a second round for my top hits using flexible residues for my receptor.
How do I prepare a ligand library for multi-stage screening? You state that you did this in the Nature paper first describing VirtualFlow.
However, I find very little information about this.
To prepare the input ligand libraries for the second stage screenings, which contain the top X compounds from the first stage, these need to be prepared manually at this point, because a random selection of the ligands to be screened is not possible at the moment. At the moment, only entire collections of ligands can be screened. We have this on our todo-list for future versions and provide scripts which automate this (if you want to work on this feature, please let us know).
In the Nature paper you did a second screen of 3 million ligands. Clearly you didn’t extract these one by one.
If this needs to be done purely manually I can extract maybe a few thousands, but it would not be great fun. Do you have a recommended protocol?