-
Hi Bokai and Shuxiao,
I would first like to thank you for developing this interesting method and making it open-sourced. I found the protein annotation and spatial pattern discovery section particu…
-
Thank you for developing Chroma. Chroma is such an excellent generative AI tool for de novo protein design.
I would like to inquire about how one can use Chroma to design new functional proteins (no…
-
Hi! Great Work!
I noticed that the carboxyl terminus of the protein is missing an oxygen atom.
Here’s an example from the demo case.
![714C877F-42F8-4570-89A3-B53D351EE7EA](https://github.co…
-
[log_2024-08-28_17-03-46.txt](https://github.com/user-attachments/files/16797894/log_2024-08-28_17-03-46.txt)
I found some old closed issues describing the same problem but there is no solution o…
-
When running the modelBasedQCPlots function, the output is missing the protein names in the title, so eg instead of "Normal Q−Q Plot ( A2AAJ9 )" it now says "Normal Q−Q Plot ( )". The plots themselves…
-
I noticed that there are some other SO term annotated that have residues. Should any of these feature be included in the feature viewer? (Show details to see the residues)
- https://www.pombase…
-
Hi, I have a corpus of about 500,000 protein sequences and would like to apply them to existing models like ESM2 or this one for predicting the fitness effect of changing an amino-acid for another.
H…
-
Hi! I noticed that in every test case, **the carboxyl terminus of the protein is missing an oxygen atom.**
Here’s an example from the demo case **demo_8ecx.**
[](url)
![8F835DD6-86D1-4d4c-8387-…
-
In setting up a variety of systems for simulation I came across one with a thioether bond (something I haven't encountered before in a protein I'm trying to simulate). The PDB structure is https://www…
-
**Issue:**
`gff2json.py` needs adjusting to allow use of new `nf-ncov-voc/assets/virus_genomeAnnotation/NC_045512.2/NC_045512.2_key.json` with aliases written as lists.
**Command:**
`python g…