The ML Engineer's Guide to Protein AI

The 2024 Nobel Prize in Chemistry went to the creators of AlphaFold, a deep learning system that solved a 50-year grand challenge in biology. The architectures behind it (transformers, diffusion models, GNNs) are the same ones you already use. This post maps the protein AI landscape: key architectures, the open-source ecosystem (which has exploded since 2024), and practical tool selection. Part II (coming soon) covers how I built my own end-to-end pipeline.