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Running `inference.py` appears to work as expected on the provided example, i.e.
`python -m inference --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_sm…
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Hi,
I recently read your work and also interested about the works related with perturbation. And I was trying to mimic your procedures for creating simulation data and ground truth.
However, I h…
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### Describe the desired behavior
It would be useful for Drug Central to have inferred drug -> drug target edges, which we could formulate as a graph ML link prediction task.
We maybe could/sho…
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Hi developer, thank you for this nice tool! I wonder can I replace swissprot/uniref/PDB with my specific set of protein? In this way, I want to compare 2 sets of my personal protein sets(search homolo…
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John relayed Frank's suggestion to use a subset of inter-residue contacts as input features for MSM-building: we would like to use just "the subset of contacts that change during a simulation." I've b…
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---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[10], line 1
----> 1 import deepchem a…
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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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Hi,
Thanks for sharing the codes and paper with us.
I was training a model with the default setting, python CPI_train.py IC50 new_compound 0.3.
From the message printed out during training, t…
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hi,
wonderful work!
According to the instructions in the README, can the target in "python pcmol/generate.py --target P29275 --device cpu" only be those included in the data/targets.txt file? If…
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In the paper it is mentioned that ), however the values reported do not seem to appear in any of the FLIP tables. What is even more confusing is that there are error bars coming from different random …