KNIME&AUTODOCK VINA

#1

Hi, everyone!

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?

 

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#2

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.

http://padel.nus.edu.sg/software/padeladv/

Alastair

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#3

Hi,

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.

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