Table 1 Allergen references and analytical parameters.
From: Three dimensional structure directs T-cell epitope dominance associated with allergy
Allergen | Ves v 5 | Api m 1 | Phl p 1 | Cry j 1 |
|---|---|---|---|---|
aka | pathogenesis-related protein | phospholipase a2 | expansin family | Polysaccharide lyase |
Source | yellow jacket | honey bee | timothy grass | Japanese cedar |
No. Residues | 204 | 134 | 240 | 374 |
Epitopes | Â | Â | Â | Â |
No. Subjects | 13 | 20 | 9 | 18 |
Peptide length | 12 | 16* | 12 | 15 |
Peptide overlap | 9 | 10* | 9 | 10 |
Step | 3 | 8* | 3 | 6 |
No. Peptides | 65 | 19 | 76 | 69 |
Reference | [2] | [54] | [55] | [56] |
Corex stability | Â | Â | Â | Â |
Structure file | 1qnx | 1poc | 1n10 | Cry j 1 model |
Reference | [53] | [57] | to be published | [58] |
Monte Carlo sampling | no | no | no | yes |
Entropy scaling | 0.994 | 0.885 | 0.85 | 1.039 |
Structure method | X-ray | X-ray | X-ray | X-ray |
Homology model, template | no | no | no | yes, 1pxz |
B-factor | Â | Â | Â | Â |
Structure file | 1qnx | 1poc | 1n10 | 1pxz |
Averaging window size | 15 | 11 | 15 | 15 |
1st derivative averaging window size | 9 | 11 | 9 | 9 |
Sequence entropy | Â | Â | Â | Â |
No. Homologs aligned | 50 | 15 | 97 | 51 |
Range of identity | 24–97% | 11–77% | 21–90% | 10–75% |
Strategy for identification | blast Genbank non-redundant | blast Swiss-Prot | blast Swiss-Prot | blast Swiss-Prot |
Averaging window size | 15 | 15 | 15 | 15 |
1st derivative averaging window size | 9 | 9 | 9 | 9 |