Running FastFloppyTail on IDPs

[Anonymous]

I don’t know if this is the appropriate place to ask this type of question but I have been reading this paper which describes the FastFloppyTail and Abinitio programs:

https://www.biorxiv.org/content/10.1101/2020.01.30.925636v1.full#F5

I am currently trying to generate 500 structures for an IDP called non-phosphorylated 4E-BP2 using the FastFloppyTail method. I used PsiPred DISOPRED3 to generate the secondary structure and disordered prediction files. I then used the Diso_SS2_Reweight_Opt_FFT.py script to reweight the secondary structure prediction based off of the disordered prediction file. I then submit my reweighted secondary structure prediction file and protein sequence into the Robetta web server to generate the 3mer fragments. I then utilize FastFloppyTail to generate the protein structures using the 3mer fragments (I am not using the -diso option, but maybe I should?).

My questions are: Do I have to use AbInitio before I use FastFloppyTail as indicated by Figure 1 in the above paper that I linked or is that only for mostly ordered proteins that have IDRs rather than an IDP? Could I supply the -t _frag option with 9mer fragments instead of 3mer fragments? 

Thanks,

Thomas 

[Anonymous]

You may need to ask the authors, I’m asking around to confirm but they do not appear to be part of RosettaCommons directly.  May I suggest opening an Issue in their Github? (https://github.com/jferrie3/AbInitioVO-and-FastFloppyTail/issues)

 

 

[Anonymous]

I have emailed the authors and if they do not respond I will open an issue in their Github. Thanks for the quick reply!

[Author]

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