-
Regarding AlphaLink 2 modeling of homodimeric protein and its complex with other protein, the inherent ambiguity of self-links in homo-multimeric assemblies poses challenges in distinguishing inter- f…
-
I created unpaired and paired MSAs using jackhmmer searches and created two separate MSA contexts out of them. However, when you combine protein complex modeling with a ligand, the AllAtomStructureCon…
-
In this project, we think we've seen an …
-
Dear all,
I am trying to create a pipeline to automate the binding energy calculation of several variants of a homotetrameric protein in complex with a medium/big-sized ligand (CoA). I haven't deci…
-
Hi, I am trying to build the mamba from the source with `pip install --no-build-isolation -e .` and it fails bc it can't find files in mamba/build/. I have no idea why.
```
g++ -pthread -…
-
Hi!
Thank you for your exciting work, and especially for sharing the data with community! I have a question about the omicsMSAs for human proteins (downloaded from [here](https://conglab.swmed.edu/…
-
Hello Yasha Ektefaie, I saw one of your Multimodal learning with graphs reviews on Nature Machine Intelligence. I have read this review very carefully. It is really an excellent article, which gives m…
-
## 🐛 Bug
This sample has many bugs, if you just try to run it, I want to propose the following fixes:
## To Reproduce
Steps to reproduce the behavior:
1. just try to run it and many exceptio…
-
## 🐛 Bug
**12 cell:**
%%time
max_epochs = 50
metric = dc.metrics.Metric(dc.metrics.score_function.rms_score)
step_cutoff = len(train)//12
def val_cb(model, step):
if step%step_cutoff!=0…
-
**Error when running:**
```
asap-ml build-dataset schnet --exp-file ~/ligand_filter_error.json \
--structures '/3c8a_complex.pdb' \
--ds-cache ~/dataset_cache_local.pkl \
--xtal…