MHC binding predictors¶
Vaxrank runs MHC binding predictors through
MHCtools. Select one with
--mhc-predictor <name>. Names marked "requires local install" need the
vendor's own executable on your PATH. The historical IEDB names also run
local tools; they do not call a web API or fall back to HTTP.
MHCflurry also needs model weights (mhcflurry-downloads fetch). Check the
MHCtools predictor guide for model
installation and allele/length support.
--mhc-predictor |
Tool | MHC Class | Notes |
|---|---|---|---|
mhcflurry |
MHCflurry | I | Open-source neural network; Python package installed with MHCtools; fetch model weights separately |
bigmhc |
BigMHC | I | Auto-detects EL or IM model |
bigmhc-el |
BigMHC EL | I | Presentation (eluted ligand) model |
bigmhc-im |
BigMHC IM | I | Immunogenicity model |
pepsickle |
Pepsickle | -- | Proteasomal cleavage predictor |
netmhc |
NetMHC | I | Auto-detects NetMHC3 or NetMHC4 |
netmhc3 |
NetMHC 3.x | I | Requires local install |
netmhc4 |
NetMHC 4.0 | I | Requires local install |
netmhcpan |
NetMHCpan | I | Auto-detects installed version |
netmhcpan28 |
NetMHCpan 2.8 | I | Requires local install |
netmhcpan3 |
NetMHCpan 3.x | I | Requires local install |
netmhcpan4 |
NetMHCpan 4.0 | I | Default mode (EL + BA) |
netmhcpan4-ba |
NetMHCpan 4.0 | I | Binding affinity mode only |
netmhcpan4-el |
NetMHCpan 4.0 | I | Eluted ligand mode only |
netmhcpan41 |
NetMHCpan 4.1 | I | Default mode (EL + BA) |
netmhcpan41-ba |
NetMHCpan 4.1 | I | Binding affinity mode only |
netmhcpan41-el |
NetMHCpan 4.1 | I | Eluted ligand mode only |
netmhcpan42 |
NetMHCpan 4.2 | I | Default mode (EL + BA) |
netmhcpan42-ba |
NetMHCpan 4.2 | I | Binding affinity mode only |
netmhcpan42-el |
NetMHCpan 4.2 | I | Eluted ligand mode only |
netmhccons |
NetMHCcons | I | Requires local install |
netmhcstabpan |
NetMHCstabpan | I | Stability predictor; requires local install |
netchop |
NetChop | -- | Proteasomal cleavage predictor |
netmhciipan |
NetMHCIIpan | II | Auto-detects installed version |
netmhciipan3 |
NetMHCIIpan 3.x | II | Requires local install |
netmhciipan4 |
NetMHCIIpan 4.0 | II | Default mode (EL + BA) |
netmhciipan4-ba |
NetMHCIIpan 4.0 | II | Binding affinity mode only |
netmhciipan4-el |
NetMHCIIpan 4.0 | II | Eluted ligand mode only |
netmhciipan43 |
NetMHCIIpan 4.3 | II | Default mode (EL + BA) |
netmhciipan43-ba |
NetMHCIIpan 4.3 | II | Binding affinity mode only |
netmhciipan43-el |
NetMHCIIpan 4.3 | II | Eluted ligand mode only |
mixmhcpred |
MixMHCpred | I | Requires local install |
netmhcpan-iedb |
NetMHCpan compatibility wrapper | I | Requires local NetMHCpan 4.1 BA |
netmhccons-iedb |
NetMHCcons compatibility wrapper | I | Requires local NetMHCcons |
netmhciipan-iedb |
NetMHCIIpan compatibility wrapper | II | Requires local NetMHCIIpan 4.3 BA |
smm-iedb |
SMM compatibility wrapper | I | Requires local SMM |
smm-pmbec-iedb |
SMM-PMBEC compatibility wrapper | I | Requires local SMM-PMBEC |
random |
Random | -- | Returns random scores; for testing only |