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Hello! Thank you for your great work of Torchdrug, GearNet, and ESM-GearNet!
Sorry to bother you. I'm trying to extract feature embeddings using GearNet (as discussed in several former issues) on EC,…
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**when I run this code**
`python datasets/esm_embedding_preparation.py --protein_ligand_csv data/protein_ligand_example_csv.csv --out_file data/prepared_for_esm.fasta `
**I met this notice:**
```
…
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Hi,
Thanks for these great resources. I have 2 questions:
1. Can you please detail what exactly are the filtering criteria used in `prune_pairs.py` and if these were already applied to the 42,826…
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Hi. I am trying to follow the documentation to install and train the model.
I have successfully installed everything and have run the following commands so far, also successfully:
bash scripts/down…
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Hi there!
How do I do inpainting on a multichain protein? For e.g. I want to make sure that all 3 chains in a trimer get the same changes. In proteinMPNN there is an option of `tied_positions` but …
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In the PDBbind2016 data directory, I see the following files that seems to be used in your training project.
`_nowat.pdb -- Receptor structure with all HETATOMS removed`
I was wonder…
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**Command that I ran:**
```
asap-ml build-dataset schnet --exp-file unknown_error.json \
--structures '*_complex.pdb' \
--ds-cache ~/dataset_cache_local.pkl \
--xtal-regex '(?
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Hello, I'm dealing with a segfault when I run:
```
python /Users/alirachidi/Documents/Sonavi_Labs/KWS/ELL/tools/utilities/pythonlibs/audio/training/make_dataset.py --list_file audio/training_list.…
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Hi!
Could I prepare the pickle file using a subset of PDB files? And so that I could search for a functional site against the subset of the PDB database. I tried the `embed_pdb_dataset.py` script, bu…
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**Describe the problem**
PROTACs are a class of therapeutics that flag target proteins to a cell's waste disposal system, instead of the traditional binding to targets. It has been very promising due…