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How do i understand the scores, like aggregate_score, ptm, iptm in the json file?
```
{
"aggregate_score": 0.4387286305427551,
"ptm": 0.7986587285995483,
"iptm": 0.34874609112739563,
"…
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Hi,
I'm trying to run hybrid ML/MM simulations of a protein-ligand system in which the ML model is used for the ligand and a handful of binding site residues. However, certain parts of the protein …
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I am getting started using AutoDock Vina, trying to check the binding of methylphenidate to the DAT receptor to check that everything is working. I am running into the following error:
```
$ vina …
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I want to run a large number of docking simulations for many ligands, and want to save each ligand's best energy without needing to read the print statements outputted to the terminal. I haven't seen …
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## *Repository Creation Request*
1. #### Coordinating Institute: Indian Institute of Technology Kharagpur
2. #### Approved Proposal: [Experimental Biochemistry](https://drive.google.com/file/…
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Hi,
Thank you very much for your Omnipath database.
Now I have some information about ligands and receptors, but I want to know what are the transcription factors and target genes downstream of…
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Hi author,
Huge fan of your work. I am currently trying to apply your code to a downstream task. Specifically, I am working with a protein PDB file and aim to extract the latent representation of the…
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https://www.biodasturchi.uz/posts/2022-09-29-ligand-docking-and-binding-site-analysis.html
Docking of various therapeutically important chemical entities to the specific target sites...
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Hi all!
This issue can be viewed in isolation / together with the other Issues I've created so far:
Issue #30 : Characterisation of the 2D protein-ligand interaction map
Issue #31 : Making a mole…
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Currently the equilibration protocol in BSIigprep.py used by the RBFE pipeline does not wrap coordinates. This makes it difficult to visually inspect equilibrates boxes to check for issues with ligand…