Seonglae ChoESM Fold, EvolutionaryScale
pip install esm
ESM 3
Protein folding prediction proceeds in two stages inside the model → AI protein folding models first create chemical relationships, then calculate spatial structure. Direct manipulation of internal representations (activation patching, steering) → enables intentional modification of protein structure. In other words, the model's internal computations are interpretable and causally manipulable
Stage 1 (early blocks) → transfers chemical information (charge, type, etc.) from amino acid sequences → to pairwise residue representations → i.e., preparation stage for "who can interact with whom"
Stage 2 (later blocks) → forms spatial information such as inter-residue distances and contacts → determines actual 3D structure