This API runs the deimmunization protocol on a given protein. Designable residues are defined with a 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

• 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

• Enable pssm model mode. Pssm model mode is enabled by default, to disable it and use the slower SVM model:

  • --pssm false

• Select the mhc config preset for pssm mode. The available options are custom and cyrus-class1-human14`. custom is the default. To change the mode:

  • --mhc-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)

Example human allele file: