I’m attempting to recapitualte ab initio results of structures published in Bhardwaj, Mulligan, Bahl et al. (2016) Nature 538(7625):329-335. doi: 10.1038/nature19791. The methods utilized a 4mer 6mer database for both design creation and ab initio structure prediction. Is this database publically available or share-able? If not, are there any considerations when attempting to make my own 4mer/6mer database (e.g. extracting the vall database sequences and creating my own 4mer/6mer set with Rosetta)?
I’m not sure that we still have the fragments themselves kicking around, but as I recall, they were generated from the vall replacing the usual 3 and 9 sizes with 4 and 6 respectively. I don’t think there was anything else special that we did, though I’ve pinged Gaurav and Chris as well — they may recall additional details.
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