Figure 3.

Interpretability of model components

(A) Diagram of attention mechanism (with attention matrix A and value matrix V) and example H3 loop attention matrix, with attention on other loops indicated. Attention values increase from blue to red.

(B) Model attention over F_V structure while predicting each CDR loop for an anti-peptide antibody (PDB: 4H0H).

(C) Key interactions for H3 loop structure prediction identified by attention. The top five non-H3 attended residues (H32-Y, L32-Y, L49-Y, L55-F, and L91-S) are labeled, as well as an H3 residue participating in a hydrogen bond (H100-S).

(D) Two-dimensional t-SNE projection of sequence-averaged LSTM embeddings labeled by source species.

(E) Two-dimensional t-SNE projects of LSTM embeddings averaged over CDR1 loop residues labeled by loop structural clusters.