Beginner needs help - SDF data export and descritor calculations

Groups Cheminformatics
1

I haven't used KNIME before but it was suggested as a good software for what I need.  I have a fairly simple task, and hope somebody can suggest a good (and relatively simple) way of doing this.

So I have a list of PubChem CIDs, some 400,000 of them, and I would like to bulk download the PubChem SDF data for all of them and to calculate select 2D and 3D chemical descriptors using CDK, and export this data into a text/csv file in a table format.

I've been googling extensively for instructions/examples of how this is done, but can't find anything relevant.  Would much appreciate any suggestions or step-by step instructions.

2

This might help:

https://tech.knime.org/forum/knime-general/workflow-examples-that-illustrate-the-chembl-restful-web-services

3

First step, for me, would be to go to the PubChem site and use the list of CIDs to download the corresponding structures.

https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi

This is probably the easiest, and quickest way. It would take a few minutes from past experience.

Once you have this SDFile, you can then use the SDFile reader  node to upload it and start using the CDK nodes to calculate the descriptors.

Hope this helps.