Changing rosetta scoring to favour less hydrophobic areas

[Anonymous]

Dear contributors,

I’d like to change the rosetta scoring function in remodel to favour models that have less hydrophobic area. Main reason is low computing power for the task at hand.

Changing fa_sol is definitely the option? Should i change the lk_ball_wtd as well?

Second thing is the assignment of secondary structure. I have clear helix propensity calculations at hand and rosetta seems to put out lots of models with wrong secondary structure even though i assigned H and L in blueprint per calculations. Should i reduce the rama_prepro or smth else?

Thanks for your time!

[Anonymous]

For design steps, I’d recommend using the aa_composition scoring term.  It allows you define “composition constraints”, each of which is a desired amino acid composition in a pose or sub-region of a pose (e.g. “I want no more than 10% alanine” or “I want 25% of residues to be valine, leucine, or isoleucine” or “I want no less than 75% polar residues”), and then to add a nonlinearly-ramping penalty for deviation from this composition.  The steps are:

– Add your composition constraints (which can be done at the commandline or with the AddCompositionConstraintMover, https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/AddCompositionConstraintMover).

– Create a scorefunction with a nonzero weight for the aa_composition scoreterm.

– Pass this scorefunction to the mover that you use for design (presumably Remodel, in your case).

In your case, you’d presumably say “I want no more than x% hydrophobic residue types in the region that I’m designing”.

Documentation is here: https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/AACompositionEnergy

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