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@ConorFWild
The CHIKV upload flushed out a bug in the algorithm, as discussed [here in Slack](https://xchem-workspace.slack.com/archives/C069ZQUN9PY/p1709678447258599):
Bug: If something …
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`Bio.codonalign` was added to Biopython about 8 years ago. Currently this module is still considered to be experimental, and prints a `BiopythonExperimentalWarning` when imported:
```python
>>> fr…
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I'm trying to implement the SCOP40 test using the latest foldseek. The `creatdb` command completes; the `easy-search` command runs for a while but then hangs indefinitely. Advice welcomed for how to i…
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Recently I tried to use MDTraj to analysis my system which is a ligand combine with a GPCR protein.Here I want to use the CA atom of GPCR protein to do the alignment and calculate the RMSD of the liga…
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Have you considered adding a wrapper for the STAMP structural alignment method? I find it does a better job with some membrane protein structures that I've been working with (using through VMD's Multi…
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Hi,
I wonder if SIFT can predict synonymous deleterious? I found some novol mutation didn't affect the aa, but with SIFT score
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Hi,
I'm new to bioinformatics and I am interested to use prospr to predict the structure of my protein of interest. I'd like to use this space to figure out how to actually run this software.
S…
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I have observed negative bits score for some pairs of protein structures in an all-against-all comparison of a collection of structures. I don't understand how this is possible, because Smith-Waterman…
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Hi!
I tried to rebuild a loop of my protein of interest using the following:
```
python /repo/RFDesign/inpainting/inpaint.py --pdb ../my.pdb --contigs A1-338,2-3,A343-585 --out RF_inpaint/338-34…