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The following report refers to the difficulties that I had when I tried to embed a GPCR to a mixed DMPC/cholesterol lipid bilayer. Specifically, parts of the protein were seriously deformed after appl…
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Hi there,
I just finished reading the paper and it was a really nice and concise model for accelerating the process of searching protein variants. When I browsed your github page, I was able to fin…
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Dear authors,
Thank you very much for making this great tool.
I got the following error while running Generate Protein Embeddings.ipynb using my protein fasta.
```
!python map_gene_symbol_to_prote…
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When I run the code on the REST API on port 6333, the below code works fine.
```python
(matches, _) = client.scroll(
collection_name="database_mock_df_flat",
scroll_filter={
…
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Hey @samsledje !
Thanks for the great work you are doing, it's really a powerful idea to apply protein-ligand similarity search for virtual screening.
According to the results of your current stat…
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Hi, there seems to be a discrepancy between the GPT models described in the paper and the ones reported in the results.
According to the paper:
> We use OpenAI GPT models corresponding to the G…
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Follow Aligning proteins wiki
Traceback (most recent call last):
File "C:\Users\work\project\structure\deepblast-master\testDeepBlast.py", line 19, in
pred_alignment = model.align(x, y)
…
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I'm looking to create embeddings for the STRING protein-protein interaction database. In this notebook, I convert this [network](https://github.com/related-sciences/string-protein-network/blob/8260123…
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Hello, about the code from bepler_embedding import embed_utils as be, where can bepler_embedding get it
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❌ create_summarized_entities
None
⠼ GraphRAG Indexer
├── Loading Input (text) - 1 files loaded (0 filtered) ━━━━ 100% 0:0… 0:0…
├── create_base_text_units
├── create_base_extracted_entities
└──…