Merge pull request #4 from trevorpfiz/platform_data_2-1

Updated data files to uncouple tooling

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

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
+                }
+            }
+        ]
+    }
+}

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

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

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

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"
+                    }
+                }
+            }
+        ]
+    }
+}

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

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"
+                    }
+                }
+            }
+        ]
+    }
+}

allergen-analysis/lbc.csv

@@ -0,0 +1,2 @@
+Peptide_Sequence,Linear_B_Cell_Immunogenicity,Linear_BCR_Recognition
+EVDPIGHLY,0.75,0.75

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
+                }
+            }
+        ]
+    }
+}