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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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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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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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Hello,
I was wondering if I can use AutoDock-Vina for docking between proteins and peptides.If not, do you have other suggestions?
Best Regards
Soodabeh
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* **PTHR ID & PTN node:**
GO:0016237 | microautophagy | IBA with PTN002244143 , S000003549
* **Sequences with problematic annotation (ID + gene/protein name):**
https://www.pombase.org/gene…
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Dear all,
The proposal has been made to obsolete GO:0019516 lactate oxidation
see https://github.com/geneontology/go-ontology/issues/27096
Experimental annotations that need to be reviewed are…
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Hello.
Thanks for this awesome work.
I have a protein-ligand system parameterized with openff. I can save it as amber format parm7 or prmtop files. But, it's not very straightforward to save frc…
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We have a homodimeric protein with chains A and B. How to define the sequence in the fasta file to be uploaded? Do we enter 1 sequence under >A, or two (identical) sequence with the same chain name?
…
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Hey there! Thank you for some amazing work. I'm wondered how can I get suboptimal RNA sequences encoding same protein? It seems like that LinearDesign will output only one sequence with best performan…
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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…