Make interactive MMP network with Knime #Knime #chemoinformatics

I posted an example that shows making interactive scatter plot with Knime. And I would like to try MMP network with Knime. I often make network view via python package such as igraph, networkx and py2cytoscape etc. BTW, today I want to learn how to do that on knime.

Recent version of Knime is provided several JS visualization nodes. So, I used Network viewrer(Js) node. And sample data is got from my githubrepo.

Now ready, I made very simple MMP generation workflow with Erlwood chemoinformatics node. The details of following screen shot is … 1 load data, 2 convert smiles to mol, 3 convert mol to rdkit mol obj, 4 Conduct MMP.


And Node8 Network creator makes empty network and Node 9 object inserter binds MMP data as network. I mapped ID-L and ID-R for node paring and Set row ID as Edge ID.

Now making network is done. Then make interactive JS plot in wrapped meta node. Screen shot of expanded meta node is below.

Two openbabel nodes convert moleculeL and moleculeR to SVG image from SMILES. Then connect Network viewer node and Table View.

Finally after running the flow, I could get interactive network view and Compound pair is shown when edges are selected.


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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