Table 1.
Summary of the top 5 predicted GPC3 peptides that could be successfully loaded onto HLA-Aa11:01 from each of the five prediction tools used for in silico analysis. Only peptides predicted by at least 3 prediction tools were selected for MD simulation.
| Peptides | Positiona | Prediction tools |
||||
|---|---|---|---|---|---|---|
| SYFPEITHI | IEDB-MHCI | NetMHC 4.0 | NetCTL | Rankpep | ||
| TTDHLKFSK | 242–250 | ✓ | ✓ | ✓ | ✓ | ✓ |
| VINTTDHLK | 239–247 | ✓ | ✓ | ✓ | ||
| KLIMTQVSK | 213–221 | ✓ | ✓ | ✓ | ||
| STIHDSIQY | 325–333 | ✓ | ✓ | ✓ | ||
| KNYTNAMFK | 123–131 | ✓ | ✓ | |||
| LQSASMELK | 93–101 | ✓ | ||||
| KLKSFISFY | 394–402 | ✓ | ||||
| PVVSQIIDK | 547–565 | ✓ | ||||
| VSKSLQVTR | 219–227 | ✓ | ||||
| VSQIIDKLK | 459–467 | ✓ | ||||
| RTMSMPKGR | 474–482 | ✓ | ||||
| NQFNLHELK | 443–451 | ✓ | ||||
| IVVRHAKNY | 117–125 | ✓ | ||||
| LLRTMSMPK | 472–480 | ✓ | ||||
Abbreviations: GPC3, glypican-3; HLA-A*11:01, human leukocyte antigen-A*11:01; MD, molecular dynamics.
a
NM_004484 was used to designate the amino acid position.