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Hello,
For a QM simulation I have to extract a protein-ligand complex binding site residues. This will create breaks in the backbone with incorrect hybridization states. The way I am trying to corr…
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First of all, thank you for the excellent tutorials and stk code. I'm a beginner at that, interested in material science mainly in extended frameworks.
I can form metal-organic cages based on paddle-…
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Hi, as clarified in the atom3D paper, the metrics for the LBD dataset is ‘-log(K)‘. Do we need to further calculate the log negative score by ourselves, or the value of `item['scores']['neglog_aff']` …
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In PPI and LBA, how do you specify the coordinate of two 3d graph? e.g., 2 proteins, ligand and target.
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https://mp.weixin.qq.com/s/W29Hy5hrDYOnLrbbEtDbUA
ixxmu updated
2 years ago
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In the ligand property of the bindingsite bb, it says:
*Ligand to be found in the protein structure. If no ligand provided,* ***no action will be executed.***
Actually, the binding site is searc…
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The tutorials need a thorough scrubbing. Let's use this issue to coordinate the needed work and sign up for fixing various tutorials.
CC @peastman @neel-shah
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Hi, I am thinking to integrate the protein structure analysis with quantitative genetics analysis. To do that, I am trying to understand folding energy better.
May I ask another stupid question, pl…
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Line 480 in receptor.py needs to be changed from:
```
super().__init__(initial_states=initial_states,
initial_weights=initial_weights,
…
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@tgbugs : we would like to add the following instances. Would you agree?
(some of them might only not exist in our list, but you have them already)
"NEW" TECHNIQUES SUGGESTIONS:
1. **calci…
lzehl updated
3 years ago