How to use KNIME for Chemical Structures

#1

Hi all,

I’m very new to Knime and I’ve been struggling to find information about how to use it. I was wondering if anyone could direct me to a good youtube video or if there is a PDF available somewhere with instructions.

My goal is to draw some chemical structures, turn them into Molfiles and then use information from this to create an algorithm to determine what rings are present in java using a javasnippet. However, I’m struggling to understand what needs to connect to what to make this happen. I attempted to draw a structure with the MarvinSketch then attached the MolConverter but now I can’t seem to attach anything to that.

Sorry for such a basic query, please let me know if you can help :slight_smile:

Thanks!
Sophie

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#2

Hi Sophie,

Start by looking at some of the example workflows on the new workflow hub (search for ‘chem’):
https://workflows.knime.com/

And also check some of the older repositories, such as MyExperiment’s cheminformatics group:
http://www.myexperiment.org/groups/125/content

If you can’t find any nodes to attach to your workflow, can I ask if you’ve installed any of the chemoinformatics nodes? There are nodes for extracting rings (just the count or whole Murcko ring systems), and a bunch of other functions that have been created by the community. To use them, install the chemoinformatics nodes from the Community Contributions repository (RDKit still has an active development group if you can’t decide which one):
https://www.knime.com/cheminformatics-extensions

If these still don’t help, post an export of your workflow here so we can see what settings you’re using in the workflow. Some nodes are a bit picky on what they expect as input.

(the other)
Simon

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