{"name":["mhci"],"version":"0.1","parameters":["input_sequence_text","alleles","peptide_length_range","predictors"],"predictors":[{"display_name":"NetMHCpan 4.1 EL (recommended epitope predictor-2023.09)","short_name":"netmhcpan_el","group":"binding","source":"binding.netmhcpan_el","has_ic50":false},{"display_name":"NetMHCpan 4.1 BA (recommended binding predictor-2023.09)","short_name":"netmhcpan_ba","group":"binding","source":"binding.netmhcpan_ba","has_ic50":true},{"display_name":"Consensus","short_name":"consensus","group":"binding","source":"binding.consensus","has_ic50":false},{"display_name":"ANN 4.0","short_name":"ann","group":"binding","source":"binding.ann","has_ic50":true},{"display_name":"SMMPMBEC","short_name":"smmpmbec","group":"binding","source":"binding.smmpmbec","has_ic50":true},{"display_name":"SMM","short_name":"smm","group":"binding","source":"binding.smm","has_ic50":true},{"display_name":"CombLib_Sidney2008","short_name":"comblib_sidney2008","group":"binding","source":"binding.comblib_sidney2008","has_ic50":false},{"display_name":"MHCFlurry 2.0","short_name":"mhcflurry","group":"binding","source":"binding.mhcflurry","has_ic50":true},{"display_name":"MHC-NP","short_name":"mhcnp","group":"binding","source":"binding.mhcnp","has_ic50":false},{"display_name":"Immunogenicity","short_name":"immunogenicity","group":"immunogenicity","source":"immunogenicity"},{"display_name":"Basic Processing Predictions","description":"predictions of antigen processing through the MHC class I antigen presentation pathway","short_name":"basic_processing","group":"processing","source":"processing.basic_processing","necessary_parameters":[{"key":"mhc_binding_method","display_name":"MHC binding method","type":"str","choice":["netmhcpan_ba","ann","smm","comblib_sidney2008","smmpmbec","pickpocket","netmhccons"],"description":"binding prediction method that provide ic50 value","default":null,"example_input":"netmhcpan_ba"}],"optional_parameters":[{"key":"proteasome","display_name":"Proteasome","type":"str","choice":["immuno","constitutive"],"description":"proteasome","default":"immuno","example_input":"immuno"},{"key":"tap_precursor","display_name":"Maximum precursor extension","type":"int","description":"The TAP score estimates an effective -log(IC50) values for the binding to TAP of a peptide or its N-terminal prolonged precursors. It has been show that high affinity of a peptide translates into high transport rates. Note that the original reference used +ln(IC50) values (ln = natural logarithm instead of log = base 10). The calculation of the score remains unchanged. ","default":1,"example_input":1},{"key":"tap_alpha","display_name":"Alpha factor","type":"float","description":"The TAP score estimates an effective -log(IC50) values for the binding to TAP of a peptide or its N-terminal prolonged precursors. It has been show that high affinity of a peptide translates into high transport rates. Note that the original reference used +ln(IC50) values (ln = natural logarithm instead of log = base 10). The calculation of the score remains unchanged. ","default":0.2,"example_input":0.2}]},{"display_name":"NetChop","description":"a predictor of proteasomal processing based upon a neural network","short_name":"netchop","group":"processing","source":"processing.netchop","necessary_parameters":[{"key":"network_method","display_name":"Prediction Method","type":"str","choice":["c_term","20s"],"description":"prediction method","default":"c_term","example_input":"c_term"}],"optional_parameters":[{"key":"threshold","display_name":"Threshold","type":"float","description":"threshold, range from 0 to 1","default":0.5,"example_input":0.5}]},{"display_name":"NetCTL (historic)","description":"a predictor of T cell epitopes along a protein sequence.","short_name":"netctl","group":"processing","source":"processing.netctl","necessary_parameters":[],"optional_parameters":[{"key":"cleavage_weight","display_name":"C terminal cleavage weight","type":"float","description":"C terminal cleavage weight, range from 0 to 1","default":0.15,"example_input":0.15},{"key":"tap_weight","display_name":"TAP transport efficiency weight","type":"float","description":"TAP transport efficiency weight, range from 0 to 1","default":0.05,"example_input":0.05},{"key":"threshold","display_name":"Threshold","type":"float","description":"threshold, range from 0 to 1","default":0.75,"example_input":0.75}]},{"display_name":"NetCTLpan (historic)","description":"an update to the original NetCTL server that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence","short_name":"netctlpan","group":"processing","source":"processing.netctlpan","necessary_parameters":[],"optional_parameters":[{"key":"cleavage_weight","display_name":"C terminal cleavage weight","type":"float","description":"C terminal cleavage weight, range from 0 to 1","default":0.225,"example_input":0.225},{"key":"tap_weight","display_name":"TAP transport efficiency weight","type":"float","description":"TAP transport efficiency weight, range from 0 to 1","default":0.025,"example_input":0.025},{"key":"epitope_threshold","display_name":"Percentile rank threshold","type":"float","description":"Percentile rank threshold, range from 0 to 100","default":1,"example_input":50}]}]}