Exploring the potential of structure-based deep learning approaches for T cell receptor design
Fig 2
ProteinMPNN and ESM-IF1 sequence recovery per CDR3 designed positions.
(A) The distribution of the percentage of sequence recovery per designed CDRα (on the left) and CDR3β (on the right) position is depicted as violin plots. Each point represents the average sequence recovery over non-redundant designed amino acids for a given test case at a given position. The position numbering follows the AHO numbering scheme. The upper bar plot shows the average over each sequence recovery distribution. Positions with fewer than three designed cases were removed for clarity. (B) ESM-IF1 sequence recovery is mapped onto the TCR structures. On the left, structures of test cases are superposed by the TCR, and only the TCR α and β chains are presented. The structures are oriented towards the pMHC plane. The CDR3β that stands out among the others is the long CDR3β from the test case 7l1d. On the right, the structures are superposed by the MHC, and only the CDR3s are shown. A representative peptide is presented as yellow spheres to highlight the orientation of the CDR3 segments in relation to the pMHC interface.