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Oxford Protein Informatics Group

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The Experimentally Relevant Future of Molecular Dynamics: Lessons from the Annual Danish Workshop on Advanced Molecu...

I recently had the opportunity to present part of my PhD work on molecular dynamics (MD) studies of engineered T Cell Receptors at the


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Chemical Languages in Machine Learning

For more than a century, chemists have been trying to squeeze the beautifully messy, quantum-smeared reality of molecules into tidy digital boxes, “formats” such as line notations, connection tables, coordinate files, or even the vaguely hieroglyphic Wiswesser Line Notation. These formats weren’t designed for machine learning; some weren’t even designed for computers. And yet...


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Some thoughts on molecular similarity

Molecular similarity is a tricky concept, mostly because there are many ways to define and measure similarity. For example, two molecules could be considered similar because they have the same biological effect, or because they have identical molecular weight, or because they contain the same functional groups, etc., etc. A natural follow-on question from this is “what is the...


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An Introduction to the Basics of Reinforcement Learning

Reinforcement learning (RL) is pretty simple in theory – “take actions, get rewards, increase likelihood of high reward actions”. However, we can quickly runs into subtle problems that don’t show up in standard supervised learning. The aim of this post is to give a gentle, concrete introduction to what RL actually is, why we might want to use it instead of (or alongside) supe...


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Dispatches from Lisbon

Tiles, tiles, as far as the eye can see. Conquerors on horseback storming into the breach; proud merchant ships cresting ocean waves; pious monks and shepherds tending to their flocks; Christ bearing the cross to Calvary—in intricate tones of blue and white on tin-glazed ceramic tilework. Vedi Napoli e poi muori the Sage of Weimar once wrote—to see Naples and die. Bu...


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