When I use openbabel to deal with a large number of ligands, I find that some results give less branches, so that I can't get better dock results.
I don't want to manually use visual software to deal with each ligand. My superficial idea is whether there is a software to add all rotatable parts to the branch.
Better suggestions are also welcome.
Then you have to use LigPrep (Schrodinger) and ConfGen to get accurate and efficient bioactive conformation.
If you are using AutoDock/Vina for docking, you can use the prepare_ligand.py or prepare_ligand4.py scripts. These scripts can be found within the installation directory of AutoDockTools (../MGLToolsPckgs/AutoDockTools/Utilities24/). PyRx probably use the same for batch processing of ligands. You can try PyRx as well.
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