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I've been trying to modify tutorial-08 to do a free energy ligand binding calculation on Bromodomain-BRD4, very similar to the one in the APR paper from 2017. With my setup, Tutorial-08 will run to co…
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Hi author,
All of my package version is same as README, but I am using a RTX 4090 GPU.
After I run this command: `python main.py --mode=0 -F=../1ypo.pdb --gpu=0 --fold=1`
I got this:
```
(gnn_d…
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Dear Author,
I hope this message finds you well.
I recently had the pleasure of reading your paper, "Learning on topological surface and geometric structure for 3D molecular generation", publish…
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Please provide as much information as you can:
MOre taxon constraints hanging around on my desktop:
apical plasma membrane urothelial plaque
A scallop-shaped plaque, also referred to as an a…
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When running the [example notebook](https://github.com/openforcefield/protein-ligand-benchmark/blob/master/docs/examples/01-protein-ligand-benchmark.ipynb) with the [production data](https://github.co…
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There appear to be some issues with how the `run_benchmarks.py` script is written: If each script is supposed to handle a transformation, which may cause issues if this code runs concurrently for mult…
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I would like to know what publications associate targets and ligands such that the publications explicitly note some interaction/relationship between the pair (not just the target or just the ligand).…
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hi ,
i downloaded the Docker image as in:
docker pull omendezlucio/deepdock
docker run -it omendezlucio/deepdock:latest
then copy/paste the source from
https://github.com/OptiMaL-PSE-Lab/D…
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# Bug description
Uni-Dock ver 1.1.2 has unstable behaviour, randomly changing its output without any valid cause. We made the following reproduction case. The behavior is similar to that with a mi…
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Dear Saeyslab team,
Thank you for creating the great package!
I have been following the vignettes for analysis of scRNA-seq data of mouse embryonic tissues. I am mostly interested in differenti…