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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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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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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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Hi Team,
Thank you for the excellent work on ESM3.
I am currently comparing the performance of ESM3 on the CAMEO and CASP14 datasets with ESMFold and AlphaFold2. The CAMEO dataset I am using is …
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Hi,
The process is automatically killed when I predicted a complex with 3000 or longer aa. But there was no problem when I use alphafold2-multimer. Could you please give me some suggestions for re…
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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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Dear author:
I try to test Fastfold, after followed the Installation Using Conda, (i think there are no command to test for a successful installation)
I run inference.py with the following code:…
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Hi, When i read the support information of AlphaFold2, I got confused about the "1.11.8 Reducing the memory consumption". It said that when using the technique called gradient checkpoint, the memory c…
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I am trying to run the alphafold2 notebook on colab pro for multimer prediction of amino acid sequences of total length 1760.
While running the prediction cell , I am getting the error as belos,
#…
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Hello,
we've been trying the updated AlphaFold2_mmseqs2 notebook hoping to be able to use AF-Multimer with a custom MSA. However setting msa_mode to custom seems to be reverting the pipeline to monom…