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[Hayes, Joseph M., and Georgios Archontis. "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular Dynamics-Studies of Synthetic and Biological Macromolecules (2012): 171-190](…
cramg updated
3 years ago
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Following internal discussion, I'm posting a quick user story here. cc @dotsdl @dwhswenson
When FE predictions are poor versus experiment, many variables can be the cause, even additively. One of t…
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A combined design pattern + template should use the same variables and dictionaries. The simplest way to do this would be via Turtle or Manchester Syntax.
Sketch of a Manchester Syntax version (co…
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The atomic convolutions currently take in an entire protein-ligand complex. This makes working with them very gnarly since proteins get large (tens of thousands of atoms easily). Since the coordinates…
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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 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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General classification for ligand activated transcription factors:
https://en.wikipedia.org/wiki/Nuclear_receptor
Dependency: Needs pattern for (DNA binding) transcription factor activity first
…
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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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I just wanted to repost the notes on what goes into a "typical protein:ligand setup pipeline" from our meeting at MolSSI on 8 Oct 2016.
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# Contributors
* John Chodera
* Julien Michel
* Peter…
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Hi, I'm trying to run the command: polygon generate \
--model_path ../data/pretrained_vae_model.pt \
--scoring_definition scoring_definition.csv \
--max_len 100 \
--n_epochs 200 \
…