-
Hello,
I am trying to setup an FMO calculation using your tool. I would like to calculate the interaction energy between a small molecule ligand and all amino acids that are 6 angstrom around it wi…
-
See the related issue (#6200) and its comments.
-
In 2014, the PDB designated SEC and PYL as standard amino acids and gave them the letters U and O, respectively. Nat made changes at the time but I think it's time to change it a little because the mm…
-
There are 2 identifiers for levdopa in NN:
PUBCHEM.COMPOUND:6047 (A small molecule)
UMLS:C0023579 (A Protein)
Levdopa is not a protein, but it is an amino acid. I suspect that this is an over-ze…
-
Hello again,
I closed the previous issue I was having as I feel we resolved this - the program ran now after I did a first assembly step to reduce the complexity of a full MGS file of raw data.
No…
-
-
Hello,
Everytime I try to predict binding of a peptide longer than 11 amino acids, I get the error : "could not broadcast input array from shape (25,20) into shape (11,20)".
Any clue how I mig…
-
- [ ] icons for all 20 canonical amino acids and protonation states
- [ ] coevolution
- [ ] salt bridge icon
- [ ] epistasis icon
- [ ] interaction network in protein
Inspiration
![image](h…
-
Hello,
Is it possible to use gapped sequences as input to kpLogo - i.e. unknown nucleotides or amino acids?
In my case, I would like to analyse k-mers across aligned antibody peptides -- each se…
-
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…