Format of output

DESCRIPTION

The prediction output consists of 13 columns.

Residue number

HLA Allele

Peptide sequence

Protein identifier

Stability prediction score

Predicted half life of the pMHC complex (in hours)

%Random - %Rank of predicted stability score to a set of 200.000 random natural 9mer peptides

Affinity Prediction score (called 1-log50K(aff))

Affinity as IC50 value in nM (only for white-listed alleles)

%Random - %Rank of predicted affinity score to a set of 200.000 random natural 9mer peptides

Prediction score combining Affinity and Stability predictions

%Rank aproximation using both, stability and affinity %Rank

Binding level (SB: strong binder, WB: weak binder)

If the "Include affinity predictions" option is set to "No", the Affinity related columns are not included into the output

OUTPUT EXAMPLES

Excluding Affinity predictions # NetMHCstabpan version 1.0 # Input is in PEPTIDE format HLA-A02:01 : Distance to traning data 0.000 (using nearest neighbor HLA-A02:01) # Rank Threshold for Strong binding peptides 0.500 # Rank Threshold for Weak binding peptides 2.000 ----------------------------------------------------------------------------------------------------- pos HLA peptide Identity Pred Thalf(h) %Rank_Stab BindLevel ----------------------------------------------------------------------------------------------------- 0 HLA-A*02:01 YIFLVSLLV PEPLIST 0.820 3.50 1.00 <= WB 0 HLA-A*02:01 ILYDVSIPP PEPLIST 0.302 0.58 8.00 0 HLA-A*02:01 YVSSILYDV PEPLIST 0.922 8.55 0.25 <= SB 0 HLA-A*02:01 FLKNSILNQ PEPLIST 0.017 0.17 34.00 ----------------------------------------------------------------------------------------------------- Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 1. Number of weak binders 1. Number of peptides 4
Including Affinity predictions # NetMHCstabpan version 1.0 # Binding affinity prediction included ( using /usr/cbs/bio/src/netMHCpan-2.8/netMHCpan ) with relative weight 0.800000 # Input is in PEPTIDE format HLA-A02:01 : Distance to traning data 0.000 (using nearest neighbor HLA-A02:01) # Rank Threshold for Strong binding peptides 0.500 # Rank Threshold for Weak binding peptides 2.000 ----------------------------------------------------------------------------------------------------- pos HLA peptide Identity Pred Thalf(h) %Rank_Stab 1-log50k Aff(nM) %Rank_aff Combined Combined_%rank BindLevel ----------------------------------------------------------------------------------------------------- 0 HLA-A*02:01 YIFLVSLLV PEPLIST 0.820 3.50 1.00 0.682 31.29 1.50 0.710 1.36 <= WB 0 HLA-A*02:01 ILYDVSIPP PEPLIST 0.302 0.58 8.00 0.510 200.19 3.00 0.468 3.43 0 HLA-A*02:01 YVSSILYDV PEPLIST 0.922 8.55 0.25 0.775 11.44 0.50 0.804 0.42 <= SB 0 HLA-A*02:01 FLKNSILNQ PEPLIST 0.017 0.17 34.00 0.166 8299.63 15.00 0.136 16.89 ----------------------------------------------------------------------------------------------------- Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 1. Number of weak binders 1. Number of peptides 4