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ChEMBL Models iPython Notebook


With the release of ChEMBL 21 has come a set of updated target predicted models.

The good news is that, besides the increase in terms of training data (compounds and targets), the new models were built using the latest stable versions of RDKit (2015.09.2) and scikit-learn (0.17). The latter was upgraded from the much older 0.14 version, which was causing incompatibility issues while trying to use the models.

I've been using the models and I thought I'd share an iPython Notebook I have created. This is based on the ChEMBL notebook with code tidbits taken from the absolutely invaluable Stack Overflow. I'm often in the situation where I actually want to know the predicted activity at specific targets, and specifically want to confirm lack of predicted activity at potential off-targets. I could have a notebook for each target but actually the speed of calculation means that I can calculate all the models and then just cherry pick those of interest.

Read on…


ChEMBL21 Update


With the release of ChEMBL21 we also get updates to the web services.

ChEMBL 21 introduced a few new tables, which are now available via the API. Keyword searching has been improved.

Compound images have transparent background by default

The official Python client library has been updated as well in order to reflect recent changes. This can be installed using PIP

pip install -U chembl_webresource_client


ChEMBL 21 released


The release of ChEMBL_21 has been announced. This version of the database was prepared on 1st February 2016 and contains:

  • 1,929,473 compound records
  • 1,592,191 compounds (of which 1,583,897 have mol files)
  • 13,968,617 activities
  • 1,212,831 assays
  • 11,019 targets
  • 62,502 source documents


Data can be downloaded from the ChEMBL ftpsite or viewed via the ChEMBL interface

Please see ChEMBL_21 release notes for full details of all changes in this release.


LSH-based similarity search in MongoDB is faster than postgres cartridge


There is a great blog article on ChEMBL-og, describing their work evaluating chemical structure based searching in MongoDB. MongoDB is a NoSQL database designed for scalability and performance that is attracting a lot of interest at the moment.

The article does a great job in explaining the logic behind improving the search performance.

They also provide an iPython notebook so you can try it yourself.


ChEMBL python update.


Excellent blog post on the ChEMBL python update.