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Input PDB file – a PDB file with the residues starting at 1 and increasing monotonically (1,2,3,4,…). Files downloaded from Cyrus Bench will be formatted in this way.
Do not include nonprotein residues.
Do not include multimodel (NMR-sourced) PDBs.
This numbering requirement is relaxed if you do not use residue sets (below).
Cyrus strongly recommends using the Prepare or Relax tool in Cyrus Bench to preprocess models before uploading to this API. This will provide a more stable scoring baseline and will make interpreting results easier.
Optional – Residue sets 1 and 2. Each list of residue indices will be allowed to form disulfides against the other group.
This is useful for a case like the inside of a beta-sandwich protein: one set is each interior face of the protein.
If you choose to supply residue set data, if there are already disulfides in your model, be sure that they are entirely inside or outside of your residue sets. Putting half a pre-existing disulfide in a residue set is forbidden behavior.
Uploaded PDBs must start at residue 1 to match this numbering scheme. If you do not intend to use residue sets, PDB numbering requirements are less strict.
If you supply no residue set data, the code will just look across the entire protein. This may be contraindicated if the protein is large (you may get too many results to sort through) or if you specifically want focussed results.
Cyrus recommends selecting residue sets, for ease of interpretation of the results.
Optional – permissive versus standard disulfide detection. Cyrus has chosen best-practice settings on your behalf. We have bundled several into one user facing option: standard versus permissive disulfide detection.
standard detection uses Rosetta’s default settings and will provide the most plausible disulfides. The downside is that it will find no plausible disulfides for some protein backbones/positions.
Permissive detection tunes the disulfide score and geometric criteria cutoffs to more permissive settings.
This means that Rosetta is much more likely to find candidate disulfides.
Many hits will be lower quality.
Many hits will appear as “not disulfides” in external software such as PyMOL – they will be oriented too poorly to be shown as a proper disulfide.
Rosetta may find a tremendous number of disulfides (or combinations thereof) for some backbones, making the results harder to interpret.
Cyrus recommends standard settings for conservative designs featuring the most likely disulfides, or permissive settings for hypothesis generation and creating large data sets for cross referencing with other tools.
Optional – Max disulfides. You can specify the maximum number of disulfides that can be created in each model produced by the disulfidizer. We recommend setting this value to 1 if you are modeling a larger protein.
Command Line Examples
Run disulfidizer on an input structure allowing any residue to form disulfides
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cyrus submit disulfidizer input.pdb --residue-set-1 "5 6 7 8" --residue-set-2 "30 31 32" |
Run disulfidizer with max disulfides set to 1
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cyrus submit disulfidizer input.pdb --max-disulfides 1 |
Python Examples
Run disulfidizer on an input structure allowing any residue to form disulfides
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