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Hi @kmayerb,
I came across a case, where two TCRs differ by an A to P change in their CDR3, but their distance is 0. How come?
```python
>>> import pandas as pd
>>> from tcrdist.repertoire imp…
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Following the Tuesday discussion, I have created a
lineage for canonical amino acid residues from
bioontology as follows:
%CHEBI:24432 biological function ontology
%CHEBI:33694 biopolymers
%CHEBI:336…
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Until now, we have only used our framework for ChEBI, but in principle, it should also be applicable to other data sets and prediction tasks. One such task is the prediction of protein functions as sp…
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i have a protein structure with some loops missing amino acids. Is there a way to use colabfold to model these loops?
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This seems (~4 years?) out of date
> Do you have plans to broaden your effort to include protein and biopolymer force fields?
> As mentioned above, we have successfully [applied for federal fund…
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The phenotype ontologies make the same classic mistake used by GO originally, in assuming CHEBI follows a biologist-friendly nomenclature. It does not. We are now undergoing an expensive refactor.
…
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As I have test that the PaRSbIP can't process many protein amino acid sequences at the same time.
What I did was that I added many amino acids sequences in the same file, but PaRSnIP only return the …
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The random_codon_table dictionary
https://github.com/modernatx/seqlike/blob/dde761ced5e3dcf86010d1e50abc3b268f794d8f/seqlike/codon_tables.py#L99
is biased for Isoleucine (I) with unequal probab…
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I have two similar proteins A and B. The only difference in sequence is about 4 amino acids. I am trying to get a specific binder recognizing A but not B. I have used the different amino acids in A as…
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Hi,In the reported paper "Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model", ``r_1912`` is the biomass production reaction in which the protein coefficient is the …