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Basically my question is: Can perses handle mutation predictions in complexes that involve a cofactor/ligand bound in one chain?
I have a system involving the study of Protein:Protein complex, usin…
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Amber can give different names to histidine amino acid by examining which protons are present : HID, HIE, or HIP instead of HIS.
This raises an issue when featurizing the protein in Diffdock becaus…
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Hi,
Thank you for developing NeuralPlexer. We ran our first attempts on a very challenging protein and we obtained promising results, most of all very different from the (useless) ones obtained wit…
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Hello,
I've tried to annotate genome with both RNASeq and proteins database. For certain genomes it worked but for some others it failed with similar errors as described in #582 and #577 (see logs …
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Hi,
I have been wondering, how does funannotate deal with gene duplications when supplying protein evidence? Ive noticed that diamond doesn't seem to allow multi mapping and therefore only one of the…
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Hi there,
first of all: great work and thanks for sharing your codebase publicly!
I wondered whether there are any plans from your end to provide a step-by-step tutorial on how to adjust the code …
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I called defense-finder run -o Typifier_results/Defensefinder_output/GCA_022437905.1_defensefinder -w 1 Intermediate_files/Genomes/GCA_022437905.1.fna
defense-finder 1.3.0 aborted with the followin…
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Hi Jon Palmer
When I use `funannotate predict` function with command `--protein_evidence A.protein.fasta`. But, there is an error indicated that `A.protein.fasta is not valid, existing`. And the `A.…
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Hi Jessica and Arthur,
In GlyGen we have protein and glycan data for medically important virus species like SARS-CoV, and HCV. We are planning to submit the data for these species however the protein…
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Hello Dr Noe,
Can you please provide an example in the notebooks demonstrating the transformation of protein into whitened Cartesian and internal coordinates?
I know that BPTI trajectory is provided…