diff --git a/allergen-analysis/cbc.csv b/allergen-analysis/cbc.csv new file mode 100644 index 0000000..1005f0f --- /dev/null +++ b/allergen-analysis/cbc.csv @@ -0,0 +1,2 @@ +Residue,ASA,RSA,N-Glycosylation,Hydrophilicity,B-Factor,Charge,Conformational_B_Cell_Epitope +31:R,67.11,0.28,0,3.0,61.24,1,0.74 diff --git a/allergen-analysis/cbc.json b/allergen-analysis/cbc.json new file mode 100644 index 0000000..1a7b75e --- /dev/null +++ b/allergen-analysis/cbc.json @@ -0,0 +1,27 @@ +{ + "Conformational_B_Cell_Epitope": { + "Inputs": { + "PDB_ID": "1A2B", + "Chain": "A", + "Prediction_Method_Selection": { + "Conformational_BCR_Recognition": "ESM3", + "Surface_Accessibility": "NetMHCPan" + } + }, + "Outputs": [ + { + "Residue": "23:K:0", + "RSA": 0.75, + "ASA": 60, + "BCR_Recognition_Probability": { + "Method": "ESM3", + "Score": 0.65 + }, + "Surface_Accessibility": { + "Method": "NetMHCPan", + "Score": 0.73 + } + } + ] + } +} \ No newline at end of file diff --git a/allergen-analysis/cbc1D.csv b/allergen-analysis/cbc1D.csv new file mode 100644 index 0000000..a138b17 --- /dev/null +++ b/allergen-analysis/cbc1D.csv @@ -0,0 +1,2 @@ +Residue,N-Glycosylation,Hydrophilicity,Charge,Conformational_B_Cell_Epitope +31:R,0,3.0,1,0.74 \ No newline at end of file diff --git a/allergen-analysis/cbc3D.csv b/allergen-analysis/cbc3D.csv new file mode 100644 index 0000000..e40441b --- /dev/null +++ b/allergen-analysis/cbc3D.csv @@ -0,0 +1,2 @@ +Residue,ASA,RSA,N-Glycosylation,Hydrophilicity,B-Factor,Charge,Conformational_B_Cell_Epitope +31:R,67.11,0.28,0,3.0,61.24,1,0.74 \ No newline at end of file diff --git a/allergen-analysis/classI.csv b/allergen-analysis/classI.csv new file mode 100644 index 0000000..cdaa58a --- /dev/null +++ b/allergen-analysis/classI.csv @@ -0,0 +1,2 @@ +Peptide_Sequence,ClassI_TCR_Recognition,ClassI_MHC_Binding_Affinity,ClassI_pMHC_Stability,Best_Binding_Affinity,Best_pMHC_Stability +EVDPIGHLY,0.63,"HLA-A*02:01=30 nM|HLA-B*07:02=50 nM","HLA-A*02:01=4.5 hrs|HLA-B*07:02=3.2 hrs",HLA-A*02:01=30 nM,HLA-A*02:01=5.0 hrs \ No newline at end of file diff --git a/allergen-analysis/classI.json b/allergen-analysis/classI.json new file mode 100644 index 0000000..59b73c4 --- /dev/null +++ b/allergen-analysis/classI.json @@ -0,0 +1,45 @@ +{ + "Class_I_T_Cell_Epitope": { + "Inputs": { + "Protein_Sequence": "MENFVLS", + "Class_I_Alleles": [ + "HLA-A*02:01", + "HLA-B*07:02" + ], + "Prediction_Method_Selection": { + "TCR_Recognition": "MHCFlurry", + "MHC_Binding_Affinity": "MHCFlurry", + "pMHC_Stability": "ESM3" + } + }, + "Outputs": [ + { + "Peptide_Sequence": "EVDPIGHLY", + "TCR_Recognition_Probability": { + "Method": "MHCFlurry", + "Score": 0.63 + }, + "MHC_Binding_Affinity_By_Allele": { + "Method": "MHCFlurry", + "Allele_Affinity": { + "HLA-A*02:01": "30 nM", + "HLA-B*07:02": "50 nM" + }, + "Best_Binding_Affinity": { + "HLA-A*02:01": "30 nM" + } + }, + "pMHC_Stability_By_Allele": { + "Method": "ESM3", + "Allele_Stability": { + "HLA-A*02:01": "4.5 hrs", + "HLA-B*07:02": "3.2 hrs" + }, + "Best_pMHC_Stability": { + "HLA-A*02:01": "4.5 hrs" + } + } + } + ] + } +} \ No newline at end of file diff --git a/allergen-analysis/classII.csv b/allergen-analysis/classII.csv new file mode 100644 index 0000000..0e8caf2 --- /dev/null +++ b/allergen-analysis/classII.csv @@ -0,0 +1,2 @@ +Peptide_Sequence,ClassII_TCR_Recognition,ClassII_MHC_Binding_Affinity,ClassII_pMHC_Stability,Best_Binding_Affinity,Best_pMHC_Stability +EVDPIGHLY,0.63,"HLA-DRB1*01:01=40 nM|HLA-DQB1*02:01=55 nM","HLA-DRB1*01:01=5.0 hrs|HLA-DQB1*02:01=3.8 hrs",HLA-DRB1*01:01=40 nM,HLA-DRB1*01:01=5.0 hrs \ No newline at end of file diff --git a/allergen-analysis/classII.json b/allergen-analysis/classII.json new file mode 100644 index 0000000..a978465 --- /dev/null +++ b/allergen-analysis/classII.json @@ -0,0 +1,45 @@ +{ + "Class_II_T_Cell_Epitope": { + "Inputs": { + "Protein_Sequence": "MENFVLS", + "Class_II_Alleles": [ + "HLA-DRB1*01:01", + "HLA-DQB1*02:01" + ], + "Prediction_Method_Selection": { + "TCR_Recognition": "MHCFlurry", + "MHC_Binding_Affinity": "MHCFlurry", + "pMHC_Stability": "ESM3" + } + }, + "Outputs": [ + { + "Peptide_Sequence": "EVDPIGHLY", + "TCR_Recognition_Probability": { + "Method": "MHCFlurry", + "Score": 0.63 + }, + "MHC_Binding_Affinity_By_Allele": { + "Method": "MHCFlurry", + "Allele_Affinity": { + "HLA-DRB1*01:01": "40 nM", + "HLA-DQB1*02:01": "55 nM" + }, + "Best_Binding_Affinity": { + "HLA-DRB1*01:01": "40 nM" + } + }, + "pMHC_Stability_By_Allele": { + "Method": "ESM3", + "Allele_Stability": { + "HLA-DRB1*01:01": "5.0 hrs", + "HLA-DQB1*02:01": "3.8 hrs" + }, + "Best_pMHC_Stability": { + "HLA-DRB1*01:01": "5.0 hrs" + } + } + } + ] + } +} \ No newline at end of file diff --git a/allergen-analysis/lbc.csv b/allergen-analysis/lbc.csv new file mode 100644 index 0000000..4d3ad18 --- /dev/null +++ b/allergen-analysis/lbc.csv @@ -0,0 +1,2 @@ +Peptide_Sequence,Linear_B_Cell_Immunogenicity,Linear_BCR_Recognition +EVDPIGHLY,0.75,0.75 diff --git a/allergen-analysis/lbc.json b/allergen-analysis/lbc.json new file mode 100644 index 0000000..234c5d5 --- /dev/null +++ b/allergen-analysis/lbc.json @@ -0,0 +1,24 @@ +{ + "Linear_B_Cell_Epitope": { + "Inputs": { + "Protein_Sequence": "MENFVLS", + "Prediction_Method_Selection": { + "Linear_B_Cell_Immunogenicity": "BepiPred", + "Linear_BCR_Recognition": "BepiPred" + } + }, + "Outputs": [ + { + "Peptide_Sequence": "EVDPIGHLY", + "B_Cell_Immunogenicity": { + "Method": "BepiPred", + "Score": 0.75 + }, + "BCR_Recognition_Probability": { + "Method": "BepiPred", + "Score": 0.75 + } + } + ] + } +} \ No newline at end of file