Deimmunizer API

The Deimmunizer API runs the Cyrus MHC Class II deimmunization protocol on a given protein. Designable residues are defined with a residue file (resfile). Multiple design runs are performed in parallel with different epitope score weights defined by the user (e.g. [0.,1.0]).

Examples

Run deimmunizer on an input structure

lev engine submit deimmunizer --pdb-file input.pdb --res-file resfile.res --min-weight 0.1 --max-weight 1.0

Run deimmunizer on an input pdb using only the alleles in the specified file.

lev engine submit deimmunizer --pdb-file input.pdb --res-file resfile.res --min-weight 0.1 --max-weight 1.0 --allele-list-file alleles.list

Inputs

  • --pdb-file
    • Input PDB file
    • CLI argument: --pdb-file input.pdb
    • Do not include nonprotein residues. Does not currently support ligands / noncanonicals.
    • Do not include multimodel (NMR-sourced) PDBs.
  • --res-file
    • Resfile defining designable residues
    • CLI --res-file resfile

Options

  • --min-weight (float32)
    • Minimum epitope score weight
    • default = 0.1
  • --max-weight (float32)
    • Maximum epitope score weight
    • default = 0.1
  • --pssm (boolean)
    • Disable/Enable pssm model mode. To disable it and use the slower SVM model set to false.
    • default = true
  • --mhc-config (str)
    • Select the MHC config preset for pssm mode (custom, cyrus-class1-human14).
    • default = custom
  • --allele-list-file (str)
    • Alleles in should be listed 1 per line
  • --repeats (int)
    • Number of designs to produce
    • default = 10

Outputs

  • aacomp.tgz
    • Deimmunizer protocol input file
    • Rosetta residue type composition energy file
    • Defines penalties deviations from desired residue type compositions during design (See References for more details)
  • svmlist.tgz
    • Deimmunizer protocol input file
    • List of SVM models for alleles being used in protocol
  • svmpssmlist.tgz
    • Deimmunizer protocol input file
    • List of PSSMs for alleles being used in protocol (if enabled)
  • svmranklist.tgz
    • Deimmunizer protocol input file
    • Ranked list of SVM models used in protocol
  • deimmunized-designs.tgz
    • Deimmunized design structures

Notes

Example human allele file:

alleles.txt HLA-DRB10101

HLA-DRB10301

HLA-DRB10401

HLA-DRB10701

HLA-DRB10802

HLA-DRB10901

HLA-DRB11101

HLA-DRB11302

HLA-DRB11501

HLA-DRB30101

HLA-DRB40101

HLA-DRB50101

HLA-DQA10501-DQB10301

HLA-DQA10301-DQB10302

References

AACompositionEnergy

Updated: