small molecule clustering and linking the online zinc15 database to search similar compounds to cluster representative

[zohaibraza]

Hello,
Part 1:
I have clustered the small molecules dataset (.sdf) by the K-medoid node. However, if i want to develop some interactive plot or graph or table for the clustering result for better visualization of results in publication. Any suggestion?
Part 2:
I want to further use the cluster representatives for similarity and physico-chemical property based compound searching in zinc15 database. So Please suggest any good knime workflow that answers the following questions:
a. How to link the zinc15 database to cluster representative for compounds search?
b. How to filter the aforementioned search with physicochemical and tanimoto similarity index?

I shall be grateful for your help! Looking forward!

Regards,
Zohaib Raza

[Martyna]

Hi,

regarding Part 1 you could check our hub for examples where k-medoids was performed and check which plots or views have been created in those workflows:

k-medoids – KNIME Hub

In case of a table containing molecules you could also create images of those molecules like in the example here:
https://hub.knime.com/knime/space/Examples/03_Visualization/02_JavaScript/08_Interactive_Webportal_Visualisation_of_Neighbor_Network
Especially the Metanode “View data” might be interesting.

Regarding Part 2: We currently don’t have an example of how to connect directly to the Zinc15 database. If you go to the hub I suggested before and search for “zinc chemistry” for example you will find workflows where zinc data was used but it has been downloaded from the zinc website before.
If Zinc does not provide any Web Services then this will be probably the only way how to work with those data - download and read in KNIME directly.

Best,
Martyna

[evert.homan_scilifelab.se]

Hi,

I don’t think ZINC15 has a webservice that can be called from within Knime so you need to download structures.

Best/Evert