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A toy model of metabolism consisting of 3-4 reactions (glucose import & subsequent conversion) will be integrated with the submodules changing protein counts np of the enzymes catalyzing the metabolic…
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Hi everyone,
I used EVM to annote my genome data using ab initio and homology protein alignment. Glancing through the results, I found the gene models that only supported by proteins were discarded…
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Here is a zoomed-in view of a region (snapshot of a web browser view). At the bottom, there is a `horizontal-transcripts` track showing Gencode v28 annotations, and we are at a scale where the protein…
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I hope I'm not missing something silly here. I'm seeing these two results for the same peptide for two different scans:
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Hi, I have a query protein sequence and I want to find orthogroup for that sequence. I don't know in howmay species its orthologues are present. How can I run orthogroup for it. What I understood from…
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Hi. First: great idea :) I've noticed a bunch of people I follow on twitter bumping this up... I wasn't confident enough to contribute in the first iteration years ago, but now I do wanna do stuff 🔥So…
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The `openFasta` (and `openFastaElectron`?) methods in Browser should try to detect if the sequence is protein, and if so, set `config.seqType="protein"` to activate @erasche's protein color scheme fro…
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If a peptide can be mapped to multiple proteins, the 1.0 specs recommend duplicating the rows, and just changing the accession. I have a strong preference to change this so that multiple accessions ca…
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Now the protein is always showed in cartoon representation it would be nice to show protein as a electrostatic colored surface. This will show more easily where the ligand is close to the protein.
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Dear authors,
I have an issue when running the script "python3.6 ../PLANET_run.py -p adrb2.pdb -l adrb2_ligand.sdf -m mols.sdf".
The error is "the protein pdb file need to be fixed" in line 21 of PL…