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Hi Patrick, thank you for sharing the Colab version of Umol. It works well and is friendly to Python freshmen. I’m just wondering if Umol can output more predicted poses (e.g., the top 10 poses), whic…
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Hi,
Thanks a lot for the wonderful work. I noticed that 'covalent modification' is [possible](https://www.chaidiscovery.com/blog/introducing-chai-1#:~:text=covalent%20modifications) to predict usin…
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Waterbridges would be an benefitial interaction addition to `ProLIF` :)
From the first glance we could use `class HBAcceptor` as an template for creating the interaction recognition. The idea that …
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Interesting paper that uses topological features plus conv-nets for protein-ligand binding. It would be cool to replicate in DeepChem and compare against atomic-convs and grid-featurized RFs on the PD…
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Scripts:
```bash
Unidock --receptor 1ipb_protein_only.pdbqt \
--ligand_index ligands.idx \
--reference ligands/M7G.sdf \
--scoring vina \
--center_x 10.671 \
…
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Thank you very much for providing such a great molecular generation model.
May I ask, does your model support protein receptors containing metal ions at binding site? I have attempted to use these …
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Hi Lin,
I was wondering what numerical integration method you chose to analyse the results after production?
Is it the Simpson rule of integration or the trapezoidal rule of integration?
Also, woul…
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Hi,
I was wondering if I could use AutoDock Vina scoring functions to evaluate protein-peptide complexes.
I used Python-based scripts from the AutoDock Vina website just for scoring the complexes.…
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**Aim:**
This issue addresses how to apply LigGrep to filter through docked ligand poses to check that they retain key interactions with the protein that are observed in crystallographic fragment-p…
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Please work to debug the step1_pdb_process.py script.
Script: https://github.com/lemaslab/CAMP/blob/master/data_prepare/step1_pdb_process.py
Input Data (RCSB PDB) : Download the fasta files fro…