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Dissecting the Hype With Cheminformatics

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A recent paper in Nature Biotechnology reported the use of AI in the discovery of inhibitors of DDR1, a kinase which has been implicated in fibrosis. Many who have worked in kinase drug discovery may have noticed that the most prominent compound (Compound 1) from this paper bears a striking resemblance to a certain marketed drug. Let's assume the compound appears familiar, but we can't specifically place it. How can we use Cheminformatics to find drugs similar to the compound highlighted in this paper? Let's take look.

In case you're interested in running the code, there is a Jupyter notebook on Github.  If you don't like code, skip to the bottom of this post for the punch line.  If you want a really easy way to run the code, try this link to a Binderized version.   This will allow you to run the notebook without downloading anything. Thanks to Peter Rose for showing me how to do this.

First, we will import the Python libraries that we'll need.  We'll also …