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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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Running our protein-prep CLI on a supported target but using a PDB structure file directly from RCSB results in a failure see the following example:
```bash
wget https://files.rcsb.org/download/5SQ…
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Hi, thank you for this approach, absolutely fascinating! I'm hoping to use this in a workflow to assess and triage eukaryotic genome annotations using FoldSeek. The range of protein sequences can be s…
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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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I will likely not implement it in #41 where I planned to because the PR is already enormous. So I write it down here.
We need to support secondary structures for cyclic proteins. Some thought were …
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The package has turned out quite clean with nice abstractions. The ideas from earlier versions have been distilled to an elegant set of types and functions, with some new additions.
The elephant in t…
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I encountered the following error while running the program. How can I resolve it? Thanks
Traceback (most recent call last):
File "../../../PLANET_run.py", line 174, in
predicted_affinit…
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For @mariacm12 `asap-genetics` pipeline we need to have a protein structure prediction pipeline. @hmacdope to investigate.
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Add a feature to candi that allows the user to retrieve sequences pertaining to a given mutation.
Will need to add functions that retrieve relevant genome builds in mutational data.
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Heyy,
I've already predicted several protein structures with Alphafold2.0 using a colab-notebook. But I have to predict around 100 protein structures and so I've heard about Omegafold wich can pred…