Macs in Chemistry

Insanely Great Science

Updated Conda


I've been checking a few things since I updated. One thing that was immediately apparent was the similarity maps in RDKit are much nicer! As you can see from the output of the HERG prediction.


Feel like I got something for free.


Accessing a Jupyter Notebook HERG model from Vortex


A recent paper "The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data" DOI described a classification model for HERG activity. I was delighted to see that all the datasets used in the study, including the training and external datasets, and the models generated using these datasets were provided as individual data files (CSV) and Python Jupyter notebooks, respectively, on GitHub

The models were downloaded and the Random Forest Jupyter Notebooks (using RDKit) modified to save the generated model using pickle to store the predictive model, and then another Jupyter notebook was created to access the model without the need to rebuild the model each time. This notebook was exported as a python script to allow command line access, and Vortex scripts created that allow the user to run the model within Vortex and import the results and view the most significant features.

All models and scripts are available for download.

Full details are here…