Exploring the potential of structure-based deep learning approaches for T cell receptor design
Fig 7
Molecular dynamics simulation analysis and binding affinity estimation with MM/PBSA of Native and ProteinMPNN and ESM-IF1 TCR designs.
(A) Box plot of calculated ΔG (in kcal/mol) of ProteinMPNN (in purple) and ESM-IF1 (in red) designs in comparison to the calculated ΔG of the native complex (green diamond) for each evaluated MHC-I test case. Each point corresponds to the median of calculated ΔG from 15 replicas. The detailed distribution of ΔG across replicas and statistical tests are presented in S25 Fig. (B) Visualization of the TCR and peptide interface from the PDB 7pdw, highlighting the interaction between R135 from the TCRα and the D4 residue of the peptide.