Who should read this

Do you want to understand exactly how AlphaFold3 works? The architecture is quite complicated and the description in the paper can be overwhelming, so we made a much more friendly (but just as detailed!) visual walkthrough.

This is mostly written for an ML audience and multiple points assume familiarity with the steps of attention. If you’re rusty, see Jay Alammar’s The Illustrated Transformer for a thorough visual explanation. That post is one of the best explanations of a model architecture at the level of individual matrix operations and also the inspiration for the diagrams and naming.

There are already many great explanations of the motivation for protein structure prediction, the CASP competition, model failure modes, debates about evaluations, implications for biotech, etc. so we don’t focus on any of that. Instead we explore the how.

How are these molecules represented in the model and what are all of the operations that convert them into a predicted structure?