Filter Out Sdf Molecules Based On Lipinski Rule

Question

[anika.menon22]

Hello,

Is there any tool that i could use to filter out sdf molecules based on lipinski rule? I have an sdf file of 10k compounds. I also have an excel sheet giving its properties (after filtering the number came down to 7k) but i do not know how i could use this to filter the corresponding sdf files.

thanks

Answer 1

[quentin.delettre]

This is a basic task that any chemoinformatic toolkit is able to do.

You can try Openbabel or RDKit for example.

Command line use of the filter option is very simple in openbabel.

Answer 2

[David Westergaard]

If you are not comfortable with a commandline tool, you can use KNIME, which has built-in nodes (both CDK and RDKit) for reading SDF files and computing properties. You'll have to get the community nodes for that, though.