Cyrus provides you with three options for disulfide modeling: Disulfidizer, Force Disulfide, and Single Chain HM. They are described in greater detail below; in this section we discuss their relative strengths, weaknesses, and purpose.
Force Disulfide is the simplest tool: it forces the input disulfide to exist and attempts to relax the protein structure in the presence of that chemical bond (simulated as bond-like restraint, not a kinematic imperative). It requires the user to state which disulfides are desired. This tool is appropriate in three cases:
- You know this bond forms in nature for this sequence (perhaps from mutational data), have a structure of the sequence without cysteines or disulfides, and want a quick peek at what it might look like
- You are doing blue-sky thinking or hypothesis generation about places disulfides could go and want to absolutely force models to have a given disulfide (our other tools will not enforce it so strongly if the energetics dislike it)
- You are creating input models for other tools like HM.
Force disulfide results should always be considered preliminary and evaluated with/after other modeling tools.
Disulfidizer is a tool for searching for disulfides. Given an input structure it will attempt to sample disulfides that might exist. This is appropriate for:
- Looking for disulfides which will stabilize the conformation of an input structure
- Searching for places to put disulfides when no prior hypothesis or suggestion is at hand
Disulfidizer results are reasonably polished (if the –permissive flag is not used), but you may wish to further evaluate disulfides with other computational tools before proceeding to a wet experiment.
Single Chain HM is a tool for generating a structure prediction for your sequence optimizing structures containing disulfides. When disulfides are well resolved in templates, Cyrus Bench’s HM tool will pick them up automatically. This tool adds an extra layer to tell Rosetta where extra disulfides are wanted by the researcher, to cover cases where the templates were not clear. This is appropriate for:
- Creating high-quality models of proteins containing disulfides that you have preliminarily modeled by other means, or have experimental reason to believe they exist
Results from Disulfide HM should be considered gold standard results from Rosetta. Further modeling never hurts but is not strictly necessary.