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Are the methods to plot the UMAP of the metagenomics dataset available?
I would like to generate a similar UMAP representation for about ~200,000 protein structures.
Any ideas where to start? Th…
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What a great job! Only the SDF files of small molecules are output in the "results/user_predictions_small" folder when I infer with the example code:
`python -m inference --protein_ligand_csv data/…
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Hi, I'm currently working on displaying multiple protein structures from their respective files. After the file is loaded initially, I would like to be able to immediately focus on a residue via it's …
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Hi guys,
when I used lollipopPlot2 to plot figure for BAGE3 gene, I got the following error.
Gene: BAGE3
Error in get_lp_data(maf = m1, geneID = gene, AACol = AACol1, refSeqID = refSeqID, :
…
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Hi there!
Thanks for this great tool - it is my first time using it (also beginner with protein structures)
I created by own prostT5 database from 345 AA seqs by doing this:
```
foldseek dat…
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In alphafold 2, they use rmsd 95 (Cα root-mean-square deviation at 95% residue coverage) to measure the similiarity of two protein structures. This metric is more stable since there are some dynamic r…
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Thank you for contributing this repository to the community!
I want to use ProSST for my own dataset. Unfortunately, my dataset only contains protein sequences (e.g., "MEAIAKYDFKATADDE") and does n…
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thank you
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Dear Foldseek Team,
I am reaching out to inquire about the possibility of developing an API to facilitate programmatic access to the data hosted on https://cluster.foldseek.com/. The ability to fe…
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Thanks for your work. However, as I tried to conduct protein structure clustering, the program always returns clusters based on proteins' substructure. I am wondering how can I get the cluster based o…