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Filter Out Sdf Molecules Based On Lipinski Rule

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

filter
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updated by David Westergaard David Westergaard • written by anika.menon22 • anika.menon22

2 answers

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.

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written by quentin.delettre quentin.delettre

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.

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written by David Westergaard David Westergaard

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