This 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]).

To get cmndline help:

• cyrus submit deimmunizer -h

Inputs

• Input PDB file – a 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.

• Resfile defining designable residues

  • CLI --res-file resfile

• Minimum epitope score weight

  • --min-weight

• Maximum epitope score weight

  • --max-weight

Command Line Examples

Quickstart

Run deimmunizer on an input structure:

cyrus 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. Epitopes should be listed 1 per line:

cyrus 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

(Requires up-to-date cyrus engine. brew update && brew upgrade cyrusbiotechnology/tap/engine)

...

• • 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:

References

AACompositionEnergy