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Gelis et al (https://doi.org/10.1002/anie.201103980) make a very good case that residues A104, F206, V260, S263, S264, and T279 are involved in ligand binding of n-amyl butyrate in OR2AG1. The article…
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Hi all!
For my project, I wish to describe the protein-ligand interactions between Mur Ligase and a known inhibitor, and hopefully, use this information to modify the molecule to extend its spectr…
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DeepChem has a number of featurization methods implemented in `dc.feat`. However, there does not exist yet a good tutorial that explains these various featurization methods. There are a lot of featuri…
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### My Question is...
[INFO ] calculating complex contribution... 53%|#########################2 | 316/600 [elapsed: 1:49:59 remaining: 3:22:20]
[ERROR ] Cal…
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I am running some tests on my system and I am getting quite high energies as for free energy of binding (~200 kcal/mol). In my current setup I am using `resid x to y` to select the ligand. Even thoug…
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Hello, glad to see your excellent work!
I encountered a TypeError: string indices must be integers when I tried to reproduce the result of protein-ligand binding affinity prediction using command `py…
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Dear Sir,
again, many thank for your work.
when I checked an example [notebook](https://github.com/HBioquant/DiffBindFR/blob/main/notebooks/AF2_model_docking.ipynb)
execution of cell 5 gave me …
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I'd like to use yank to calculate binding free energy for a peptide binding to a protein. I couldn't find any examples of this, so I'm not sure if this is a supported use case, but I gave it a try an…
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Contrary to the AlphaFold3 server, we now can include water molecules as ligands. Using ccdCodes works really well (and probably water smiles work too, but I have not tried) :
`"ccdCodes": ["HOH"]`…
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After reading your documentation I didn't find a script that will tell the docking software to bind a ligand in a specific area/residues desired. Can you help me in that?