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]).

Command Line Interface

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

Flags

  • --allele-list-file (str) (Optional)
    • Path to a file with one allele name per line
  • --max-weight (float32) (Default = 0.1)
    • Maximum epitope score weight
  • --mhc-config (str) (Default = custom)
    • Select the MHC config preset for pssm mode (custom).
  • --min-weight (float32) (Default = 0.1)
    • Minimum epitope score weight
  • --pdb-file (str) (Required)
    • Input PDB file
    • Do not include nonprotein residues. Does not currently support ligands / noncanonicals.
    • Do not include multimodel (NMR-sourced) PDBs.
    • You can specify this flag as the first positional argument or with the --pdb-file flag
    • Examples:
      • "input.pdb" - Local PDB file
      • "structures/protein.pdb" - PDB file in subdirectory
      • "/path/to/structure.pdb" - Full path to PDB file
  • --pssm (boolean) (Default = true)
    • Disable/Enable pssm model mode. To disable it and use the slower SVM model set to false.
  • --repeats (int) (Default = 10)
    • Number of designs to produce
  • --res-file (str) (Required)

Python Interface

Examples

Run deimmunizer on an input structure

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_deimmunizer(
    pdb_path="input.pdb",
    resfile_path="resfile.res",
    min_weight=0.1,
    max_weight=1.0
)

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

job_id = client.submit_deimmunizer(
    pdb_path="input.pdb",
    resfile_path="resfile.res",
    min_weight=0.1,
    max_weight=1.0,
    allele_list=["HLA-DRB10101", "HLA-DRB10301"]
)

Flags

  • allele_list (List[str]) (Optional)
    • List of alleles to use in the design
    • Examples:
      • allele_list=["HLA-DRB10101", "HLA-DRB10301"]
  • max_weight (float) (Default = 0.1)
    • Maximum epitope score weight
  • mhc_config (str) (Default = custom)
    • Select the MHC config preset for pssm mode (custom).
  • min_weight (float) (Default = 0.1)
    • Minimum epitope score weight
  • pdb_path (str) (Required)
    • Input PDB file
    • You can specify this flag as the first positional argument or with the --pdb-file flag
    • Examples:
      • "input.pdb" - Local PDB file
      • "structures/protein.pdb" - PDB file in subdirectory
      • "/path/to/structure.pdb" - Full path to PDB file
  • pssm_mode (bool) (Default = true)
    • Use PSSM mode for deimmunization
  • repeats (int) (Default = 10)
    • Number of designs to produce
  • resfile_path (str) (Required)
    • Path to a Rosetta resfile
    • Resfile defining designable residues
    • You can specify this flag as the second positional argument or with the --res-file flag

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: