Hi,
Thank you for this tool. I'm using a 5070Ti GPU/Cuda12.8/torch 2.7.1 and it works very well.
The only thing is that Unidock is using Vina scoring function which rewards ligands that fit very well in the pocket (hydrophobic/packing) more than molecule having good anchor points like Hbonds, metal coordination,... which are linked to specificity and activity.
Recently, a fork of Unidock was published: Unidock Pro. It has an hybrid mode rewarding molecules that bind like a reference ligand. This is a nice way to get around the problems linked to vina's scoring.
I'm currently trying to modify RxnFlow to switch from Unidock to Unidock Pro but it is really difficult for me as I do not know all the details behind RxnFlow.
If you want a suggestion for future updates, this is one that would be great ... updating to Unidock Pro. It would integrate binding mode during the training and generation of ligands. Now I'm using filtering post-generation but I need to generate something like 1M molecules to get a few that interact like a drug.
Thanks
Hi,
Thank you for this tool. I'm using a 5070Ti GPU/Cuda12.8/torch 2.7.1 and it works very well.
The only thing is that Unidock is using Vina scoring function which rewards ligands that fit very well in the pocket (hydrophobic/packing) more than molecule having good anchor points like Hbonds, metal coordination,... which are linked to specificity and activity.
Recently, a fork of Unidock was published: Unidock Pro. It has an hybrid mode rewarding molecules that bind like a reference ligand. This is a nice way to get around the problems linked to vina's scoring.
I'm currently trying to modify RxnFlow to switch from Unidock to Unidock Pro but it is really difficult for me as I do not know all the details behind RxnFlow.
If you want a suggestion for future updates, this is one that would be great ... updating to Unidock Pro. It would integrate binding mode during the training and generation of ligands. Now I'm using filtering post-generation but I need to generate something like 1M molecules to get a few that interact like a drug.
Thanks