How to bulk download properties from chemicalize.org

Hi,

I am looking for a way to download the calculated properties for all chemicals on the site in a bulk download, so that I can query them from a perl program that I have written. Is there a way to do this?

Thanks!

Hi Sujaya,

We don't store the calculation results, so I cannot give this data.

I could however give you the molecule database itself (~340k structures) as a SMILES or MRV or SDF and you could perform calculations and analysis yourself.

Would that help you?

Andras

Hi Andras,

Thanks for the prompt response. Yes, it would help to have the database of molecules in SMILES format, and then I could perform the calculations. Is there a way you could provide this?

Thanks!

Hi Suyaja,

http://www.chemicalize.org/downloads/chemicalizeorg-structures.smi.zip (2.5MB)

If you come to any interesting conclusions from analysing this dataset, we would really love to hear about it. Also I should mention that if you publish any scientific articles/create presentations based on this data, we would love it if you could cite ChemAxon and chemicalize.org.

https://www.chemaxon.com/forum/ftopic977.html

Enjoy!
Andras 

Thanks for the link to download. I see that the downloaded file has only SMILES strings. Is there an easy way to get pubchem ID (if it exists) for these strings, since that is what I would like to index by? 

I will certainly acknowledge chemicalize and chemaxon if we do use and publish anything. 

Thanks again!

If you're interested in the pubchem IDs, I recommend downloading the chemicalize.org structures from pubchem. We are a datasource on pubchem for a few months now.

http://www.ncbi.nlm.nih.gov/pcsubstance?term=%22954%22%5Bsourcename%5D&cmd=search&db=pcsubstance

BR,
Andras 

That's wonderful that there's a database (?) with ~340,000 compounds listed.  That .smi file extension has me baffled, though: what is it and how do I open such a file, please?  Thanks.

Thanks for the question.