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alphafold feature generation #18
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Sorry, there is currently no plan to open source the feature generation code. (It's tightly coupled to our internal infrastructure as well as external tools which we cannot open source.) However, I updated the README with descriptions of all the features. I also added code snippets that show how to calculate most of the features that are needed. I hope this helps. |
Why the pseudolikelihood estimation parameters have 484 (=22*22) parameters instead of 441 (=21*21) parameters? Almost all potts model implementation only has 441 parameters for each residue pair. Is it possible to release AlphaFold's pseudolikelihood estimation pipeline? |
I guess they used 20 amino acid types + X + gap. |
Thank you for sharing some code snippets for the input feature generation.
can be converted into A3M format (by using HHsuite reformat.pl) as
Since those deletions in Templ_1 (yw) and Template_2 (fw) are aligned(?) to the gaps in the Query sequence, the deletions would not be counted. |
Hello,
I'm interested in the details about feature generation described in the method section of the paper. Is there a plan to open source the script for generating the features from MSA data? or is it already exist, just that I didn't see it.
Thanks!
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