Is the molecule in the computer?

The Molecular Graphics and Modelling Society began life as the Molecular Graphics Society. It’s hard to imagine a time without computer graphics, but yes, it existed. The MGS was formed by the pioneers who made molecular graphics commonplace.

In 1994, the MGS organized an Art and Video Show (Goodsell et al., 1995), and I submitted some of my own work. One of the other images — inspired by Magritte‘s “Ceci n’est pas une pipe”, depicts a molecule with a remarkable similarity to a pipe — and to a molecule… It was submitted by Mike Hann (of GSK):

“Ceci n’est pas une molecule”, image by Mike Hann, 1994.

It aptly questions, what is a molecule, and to me, highlights one of the central questions of our own research: what’s the best way to represent a molecule computationally?

In many ways, when it comes to algorithm design, and especially machine learning and deep learning, how we represent a molecule (or a molecular system) determines what our models can ‘perceive’. In many ways, our input representations can strongly influence the inductive biases we supply, the amount of data needed to train our models, their ability to generalize, and their resultant accuracy.

References

Goodsell, D. S., Larsen, T. A. & O’Donnell, T. J. 1994 Molecular Graphics Art Show and Video Show. J Mol Graph 13, 223–41 (1995).

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