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Hello, I am using this project to predict the docking pose of cyclic peptides with proteins. I am using several examples from the original paper, such as 1SFI and 3AV9. The input format is in the form…
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**Describe the bug**
A user has queried why the variant description `NM_000059.4:c.[1916dup;1929del]` is handled as two separate variants for the purposes of validation: `NM_000059.4:c.1916dup` predi…
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## Expected Behavior
I used colabfold to predict two monomer proteins cas9 and deaminase, and I wanted to continue to predict their possible complex structure by multimer method.
While the cas9 p…
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https://github.com/griffithlab/pVACtools/blob/7c4b383c554a62352c74a92884bc5214267810b1/pvactools/tools/pvacseq/generate_protein_fasta.py#L45C1-L48C6
The `generate_protein_fasta.py` script uses the …
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Hi,
I want to run "mmseqs easy-rbh" on all pairs of a large dataset of genomes (let's say 100 genomes, so 10,000 pairs). I tested on 1 pairs and it took 27 seconds to run.
I thought to use the mod…
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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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I was just wondering is it possible to get the importance score of the protein sequence using EvoProtGrad model? For instance, in https://huggingface.co/datasets/waylandy/phosformer_curated data there…
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Hi!
I am using Hmmer3 with bivalve genomes looking for 70-80 aa genes. BUSCO scores for the genomes are in the upper 90s (96-98% complete for BUSCO Metazoa) and most assemblies are chromosome-scale…
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Jan 30 09:37:01 ..... started STAR run
Jan 30 09:37:01 ... starting to generate Genome files
Jan 30 09:37:38 ... starting to sort Suffix Array. This may take a long time...
Jan 30 09:37:49 ... sort…
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def two_prot_inter_sort(df,column_protein_1,column_protein_2,column_val, seuil_min, seuil_max=1) :
protein_1_list=list(set(list(df[column_protein_1]))) #on initisalise les listes des prot…