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Dear Dr. Oliver,
Thank you for the very nice program. I was wondering:
Assuming we have a predetermined small secondary RNA structure we want to designate as the binding pocket, is there a way t…
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it would be great to create a `skbio.io.format.pdb` and associated `skbio.structure` to handle protein/RNA structure files in PDB and mmCIF formats.
I think it would nicely complement sequence object…
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This came up unexpectedly during #3121, where we noticed that parsing PDB files via SeqIO assumed them to be protein.
However, PDB files can contain RNA, DNA, protein (or mixes). e.g. https://www.r…
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Hi there
I'm recently developing [MultiMolecule](multimolecule.danling.org), and we have included many pre-trained foundation models in our hub.
I believe RibonanzaNet can be an excellent addit…
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- [ ] Datasets
- [ ] AlphaFold 3 PDB dataset
- [x] PDB mmCIF filtering script (`scripts/filter_pdb_mmcifs.py`)
- [x] Fix periodic residue count-chemical component coun…
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Is the NSP library still downloadable? I have an old copy of the library, but there is no
"/RNA/pars/cg/CG2AA/templates2.pdb"
within the library, causing ``nsp optimize`` to fail.
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First of all, thanks for your work !
### Setup
I am reporting an improvement in Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
…
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I ran this program successfully, but the output PDB file does not look right. The last amino acid of the protein is connected to the first RNA base. Is there a way to fix this?
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Hi, thanks for your amazing work
I wanted to ask about sharing the training code and data?
for RNA/DNA data all of the thing I see in repo are sequences. could you please share pdb files
Than…