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Scoring function for disordered peptide ddG calculations?

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Scoring function for disordered peptide ddG calculations?
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I am looking to do a ddG analysis on some peptide structures that I have developed through simulation. Previously, I have used pyrosetta for performing ddG analyses on membrane proteins. In that case, I was able to use the franklin_2019 weights as my scoring function.

Poking around, I have seen that there are a good number of weights files listed as:
/PATH/pyrosetta/lib/python3.9/site-packages/pyrosetta/database/scoring/weights/*.wts

I know from my experience that there is a function specific for membrane proteins, and that there is something like a default scoring function in REF2015 (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/score-types). Is there any documentation to point out specific scoring functions for different applications, including disordered proteins or peptides?

Thanks,

Austin Weigle

 

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Tue, 2024-05-28 14:52
austin.weigle.usda

I'm not sure if there's any particular scorefunctions which have been optimized for modeling disordered peptides as disordered peptides. The standard soluble Rosetta score function would probably be your best choice.

If you're modeling the disordered peptide in complex with a structured protein, then I would look at it more as a peptide binding problem, rather than a disordered peptide modeling problem. Take a look into the FlexPepDock protocols.

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Thu, 2024-06-20 11:22
rmoretti