Predicting and designing proteins (1): How protein structure became a computational problem

Recently I’ve been working on predictive and generative models of proteins. Quite a shift in expertise, if you ask me! Therefore, I may as well write some literature review posts about proteins here. (Not that I have no more SWE knowledge to share, and not that AI has fully replaced us for non-cutting-edge material to write about. Well... 🙁) P.S. I’m sorry for not updating anything since March; consider this series me making good on my earlier promise to update more often. A protein is a chain whose units are called amino-acid residues. “Residue” is the conventional name for an amino acid after it has been joined to the chain. Each residue has the same backbone pattern and one of twenty common side chains, which differ in size, charge, flexibility, and chemical reactivity. The order of those residues is the protein’s sequence. The chain can bend around its backbone bonds, bring distant residues together, exclude water from some regions, expose other regions to solvent, and form a…