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Hi, I've been running the MMseq2 ColabFold for a specific type of protein sequences, and I always get the same set of ~4000 sequences in the .a3m file. Would it be possible to put these sequences from…
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We are running the following protein sequence with AlphaFold2-ptm, using the AlphaFold2_mmseqs2 notebook. It is approximately 629 AA long. I have a Colab Pro account, so RAM should not be an issue for…
gezmi updated
2 years ago
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Hi,
I am interested in using ftdmp to see if it improves the predictions of antibody vs antigen pairs I have attempted so far with Alphafold2-multimer and Unifold. Is there or could there be a Cola…
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1.According to this paper Buel, G.R., Walters, K.J. Can AlphaFold2 predict the impact of missense mutations on structure?. Nat Struct Mol Biol 29, 1–2 (2022). https://doi.org/10.1038/s41594-021-00714-…
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Hi,
I tried running AlphaFold2_mmseqs2 on these two files separately:
```
>HHAWx4
HHAWHHAWHHAWHHAW
```
And
```
>KKAWx4
KKAWKKAWKKAWKKAW
```
Although the sequences are valid ami…
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## Expected Behavior
Don't crash on envdb when sequence length is less than 12 aa long (for example on `SEGGQDFWL` or `GSSGLISMPRV`).
## Current Behavior
MMseqs2 process crashes on aligning…
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Hi,
I tried your pipeline several times but I never get to the end because no files are left.
I first tried the notebook as is, but then I had to change filter values such as SASA_limit when anayl…
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Hello,
The .ipynb script works correctly for .a3m files generated from ColabFold; however, when I try to use the generated files in AlphaFold2 version 2.3, I get the following error message:
Tr…
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### Description of feature
Jalview is a free cross-platform program for multiple sequence alignment visualisation and analysis. Its integration into the AlphaFold2 and Colabfold workflows of the pipe…
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Hi! After running openfold according to the default configuration, I found that there was a big difference between the output pdb file of openfold and alphafold (colab version). After comparing the re…