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4mer 6mer fragment database

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4mer 6mer fragment database

Hi everyone,

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)?



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Wed, 2020-09-09 15:12

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.

Wed, 2020-09-09 17:58

Thank you for the help Vikram! Looking forward to any additional details.


Wed, 2020-09-09 20:04