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FoldX DDG calculation: how to allow for (limited) backbone movement?

I have a protein with a L-->H on a buried residue.

I would like to estimate the DDG between this MUT and the WT using FoldX.

Currently I'm using the command:

foldx --command BuildModel --pdb ${modelname}_Repair.pdb --mutant-file individual_list.txt --numberOfRuns 5

Unsurprisingly, the predicted stability change is high. However in exploring the models, I see that this default behavior only takes into account the effects the MUT has on the sidechains. I'd like to also allow for some local backbone movement to more fully explore how the MUT could affect my energy estimates.

Is there an option in FoldX to allow for this? (I'm not finding the official FoldX documentation easy to search)

Thanks for any help

protein foldx stability gibbs ddg
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written by darink • darink

1 answer

This is a command I use:

foldx --command=PositionScan --pdb=your_file.pdb --positions=LA18H --output-file=OUT

The --positions switch means leucine in chain A and position 18 to histidine. It moves the neighboring residues as needed, though it still may be only their side-chains.

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written by Mensur Dlakic Mensur Dlakic

Thanks. Just tried this and the dihedrals are still identical.

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written by darink • darink

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