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Hi @ppxasjsm from discussions with @maxkuhn it is also good to clarify
- why the R_mean value from X resampled calculated free energies is always lower than the R value of the original dataset
…
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MDtraj doesn't recognize my system (Ligands + water + Na Cl + POPE, 310K, 50 ns) after executing in Jupyter Notebook:
traj = mdtraj.load_dtr('desmond_md_jesus103_trj/clickme.dtr',top='topology.pdb'…
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Hi,
I tried to prepare `*_rigid.pdbqt` and `*_flex.pdbqt` files for flexible docking with vina, and then noticed that errors occur when some input PDBQT files are used with the command below.
``…
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In trying to train ProteinBert, I've received the following error:
```
indices[31,1] = -127 is not in [0, 290)
[[{{node model/embedding-seq-input/embedding_lookup}}]] [Op:__inference_train_functi…
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Dear GraphscoreDTA developers,
Thank you for the excellent work. However, I was wondering how the trained model can be used to predict protein-ligand binding affinities for a protein-ligand pair th…
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**Description:**
- DeepChem Version: 2.1.0
- Platform: Ubuntu 16.04
I am following the Predicting Ki of Ligands to a Protein tutorial (https://deepchem.io/docs/notebooks/BACE.html), on …
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Hello and Happy New Year!
Once again, thanks for such a great tool. I wanted to ask a quick question because I couldn't find it in the couple vignettes I was working through. I was wondering if you…
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The app becomes sluggish when opening large models (like 4UG0). Some observations:
- Hovered residue search algorithm spends a lot of time looking for the hovered residue.
- `mc.get_ligand_svg` is cal…
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Dear GPCRdb team,
We are looking at this specific file named [cs.tv](https://github.com/protwis/gpcrdb_data/blob/master/structure_data/cs.tsv) in your repo and are unable to understand what this su…
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Hi Althea and team,
I used -mfpc and -ifpc with the last version of Ringtail (v1.0.0), I was able to apply both filters with warning that the interaction filter would be applied first and then morg…