How best to perform an automated virtual screening against a small molecule database with Autodock Vina and KNIME? Or use Raccoon( http://autodock.scripps.edu/resources/raccoon)
I have sdf file and convert to pdbqt.
Can someone suggest some node? Or give an example?
you might be able to use PADEL-ADV command line version in an external tool node, although it might require some high level techfu to get that working properly.
I don't know if this is still a topic of interest, but in case someone wants to try a Pythonic alternative, the attached workflow did fine for a couple of tests I ran. Python, some libraries and AutoDock Vina have to be installed and the environmental variables have to be set as well.
I hope this helps someone.
Let me know what you think.