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 engine submit deimmunizer -h

Inputs

...

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.

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

  • 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

• --

  min

  max-weight (float32)

  • Maximum epitope score weight

  • default = 0.1

• --

  max-weight

  pssm (boolean)

  • Disable/Enable pssm model mode.

  Pssm model mode is enabled by default, to

  • To disable it and use the slower SVM model

  :

  • --pssm falseset to false.

  • default = true

• --mhc-config (str)

  • Select the

  mhc

  • MHC config preset for pssm mode

  . The available options are custom and

  • (custom, cyrus-class1-human14

  `

  • ).

  custom is the default. To change the mode:

  • default = custom

• --

  mhc

  allele-

  config cyrus-class1-human-14

Command Line Examples

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

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

• 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