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Hi,
Thanks for this code, it is very interesting.
To install and run I had to make a few modifications to the install instructions:
Firstly install torch and other torch packages along with a…
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The gff files I'm seeing contain multiple hits to the same gene, and I'm trying to figure out if they are actual gene duplications or if they are duplicates because of assembly/read issues. For examp…
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Dear developers,
I am encountering an issue with peptide-shaker, which I paste here:
# ------------------------------------------------------------------
# PeptideShaker 2.2.25 Report File
#
…
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I get this error after extracting the 'sdf' field from the ligands.json file included in the repo, I get it with quite a few of molecules. I can run peptide/nucleotide inferences without issue. Any id…
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Hi, congratulations on the excellent work! The publication was highly engaging, and the results are very promising. I have a question about how DynamicBind processes ligands, specifically regarding it…
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We are working on Chignolin Coarse Grain Tutorial from this repository:
https://github.com/torchmd/torchmd-cg.git
We are working on a Machine Learning project pertaining to Coarse-graining of prot…
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Thank you for your fantastic works, but I cannot run protein example.
I tried change directory name by `mv UniRef30 uniclust`, replace "DB_UR30="$PIPE_DIR/uniclust/UniRef30_2021_06" to "DB_UR30="$PI…
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In rf2aa/preprocessing.py the path to the make_msa.sh command is prefaced with a "./" :
search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}"
…
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I would like to perform batch inference. Can you please point me some resources or provide support for it? Thanks a lot
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Hello,
As per [this line](https://github.com/aqlaboratory/openfold/blob/main/openfold/model/evoformer.py#L649), when neither Deepspeed nor LMA is selected, the custom memory-efficient [kernel](http…