Chapter 5. Biophysical Machine Learning

In this chapter, we will explore how to use deep learning for understanding biophysical systems. In particular, we will explore in depth the problem of predicting how small drug-like molecules bind to a protein of interest in the human body.

This problem is of fundamental interest in drug discovery. Modulating a single protein in a targeted fashion can often have a significant therapeutic impact. The breakthrough cancer drug Imatinib tightly binds with BCR-ABL, for example, which is part of the reason for its efficacy. For other diseases, it can be challenging to find a single protein target with the same efficacy, but the abstraction remains useful nevertheless. There are so many mechanisms at play in the human body that finding an effective mental model can be crucial.

Drugs Don’t Just Target a Single Protein

As we’ve discussed, it can be extraordinarily useful to reduce the problem of designing a drug for a disease to the problem of designing a drug that interacts tightly with a given protein. But it’s extremely important to realize that in reality, any given drug is going to interact with many different subsystems in the body. The study of such multifaceted interactions is broadly called polypharmacology.

At present, computational methods for dealing with polypharmacology are still relatively undeveloped, so the gold standard for testing for polypharmacological effects remains animal and human experimentation. As computational techniques ...

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