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Thanks for this great package!
I would like to make a ligand-receptor-target circos plot as described in the "circos" vignette and as seen in "B":
![circos plot with summary](https://user-images…
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Running our protein-prep CLI on a supported target but using a PDB structure file directly from RCSB results in a failure see the following example:
```bash
wget https://files.rcsb.org/download/5SQ…
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Dear Saeyslab Team,
Thank you for the amazing package.
I am encountering an issue where running the same code with identical input data in both RStudio and on a server yields different numbers o…
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The current version requires:
>
> For each complex you want to predict, you need a directory containing the ligand and protein file. For example:
>
> ```
> DSDP_dataset
> └───name1
> │ …
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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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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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[ASAP-0015381](https://github.com/StructuralGenomicsConsortium/CNP25-CHIKV-nsP3-Macrodomain/assets/133207721/fca7cc25-1a3e-4edc-8abf-217449838c4c) is One of the ASAP potent inhibitors vis SARS-CoV-2-N…
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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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It seems like some annotations contain upstream proteins that should be annotated to 'regulation of NF-kappaB signal transduction' and/or using the relation 'acts upstream of or within' for the NF-kap…
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Dear all,
I'm experience the following mistakes:
1) I have prepared my system using charmm-gui (protein-ligand). when I run the equilibration step the target temperature is in average 309 K (m…