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AlphaFold DB proteome subset #24

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kad-ecoli opened this issue Mar 25, 2023 · 3 comments
Open

AlphaFold DB proteome subset #24

kad-ecoli opened this issue Mar 25, 2023 · 3 comments
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enhancement New feature or request

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@kad-ecoli
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kad-ecoli commented Mar 25, 2023 •
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Is it possible for https://foldcomp.steineggerlab.workers.dev/ to distribute the subset of AlphaFold database corresponding to the "Model organism proteomes" and "Global health proteomes" listed by https://alphafold.ebi.ac.uk/download?

Many of these proteins are not from swissprot and therefore not in a afdb_swissprot_v4.
@khb7840 khb7840 added the enhancement New feature or request label Mar 26, 2023
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khb7840 commented Mar 26, 2023

Thank you for notifying that. We'll upload those soon.

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khb7840 commented Mar 27, 2023

We uploaded model organism proteomes and you can download them with foldcomp.setup('h_sapiens'), foldcomp.setup('a_thaliana') or foldcomp.setup('e_coli') in python.

Global health proteomes will also be uploaded soon.

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khb7840 commented Mar 29, 2023

Current version of database contains both CIFs and PDBs. We'll upload processed version soon.

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@kad-ecoli @khb7840