Exploring the potential of structure-based deep learning approaches for T cell receptor design
Fig 5
Maximum sequence recovery of interface CDR3s amino acids in the presence or absence of pMHC structures.
(A) Bar plot displaying the maximum sequence recovery for each test case, with designs generated by ProteinMPNN shown on the top and those by ESM-IF1 on the bottom. Colored bars (purple or red) represent the CDR3 interface designs considering the corresponding pMHC complex, while grey bars represent the interface design of unbound TCRs without the pMHC. (B) Same as (A), but grouping together the maximum sequence recovery values for ProteinMPNN with pMHC, ProteinMPNN without pMHC, ESM-IF1 with pMHC, and ESM-IF1 without pMHC. Statistical comparison between groups were performed using Mann-Whitney test with the R ggpubr package. Significance is indicated above each box plot (**** and *** correspond to a p-value below 0.0001 and 0.001, respectively, while ‘ns’ means no significance (p- value ≥ 0.05)). (C) Scatter plot with a linear trend line and a 95% confidence interval (light blue region) illustrating the correlation between the difference in maximum sequence recovery upon pMHC removal (maximum sequence recovery with pMHC minus sequence recovery without pMHC) for ProteinMPNN and ESM-IF1. A dashed diagonal line is included to aid in visual comparison. The correlation coefficients are indicated in the plot.