-
I try to execute the following line:
```python
ogb_dataset = NodePropPredDataset(name="ogbn-proteins", root=f"{datasets/data/ogb")
```
This starts off doing what it is supposed to:
- it downloa…
-
Hi,
As I understand it one of the end goals of ESPALOMA is to be able to parameterise an entire system without the need for individual residue templates (what got me excited about it in the first p…
-
Hi, recently I buy lot of memory to do bigger structure interactions, and I have the impression Alpha Pulldown cannot take more than 10 proteins (here 20). Maybe it's cause the name is too long ?
T…
-
Hi all
I'm interested in generating contact maps from the ESM2 attention heads as described in the following github notebook:
https://github.com/facebookresearch/esm/blob/main/examples/contact_predi…
-
Hi.
I did the protein-protein interactions (PPIs) analysis and I have the csv file now after I melted the results. Now, I am wondering how can I filter the PPIs based on their location, limited to …
-
I don't think that we parse correctly the ions in FragPipe.
In the .toml, I see this:
```
[mapper]
"Peptide Sequence" = "Sequence"
Protein = "Proteins"
Charge = "Charge"
```
So do we complete…
-
See https://github.com/NCATSTranslator/Feedback/issues/613 https://github.com/NCATSTranslator/Feedback/issues/614 https://github.com/NCATSTranslator/Feedback/issues/615.
These are all proteins, whi…
-
Hi,
This is regarding protein generation in DiG.
I wanted to know how you obtained the features present in the protein pickle files. As per Appendix B.1 of the paper, the single and pair represe…
-
Your work is excellent, and I want to design small molecule binding proteins with your moldes. But I'm afraid I can't understand the meaning of these parameters, after consulting Extended Data Fig. 6 …
-
Hello dear BRAKER developers,
1. I want to annotate a fungal genome for which I do not have RNA-seq evidence, so I intend to use proteins as evidence, however, I have doubts about how to use this o…