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**Is your feature request related to a problem? Please describe.**
I was trying to prepare a system with a protein and 2 ligands (given as SDF files).
However, both ligands were named "MOL" and bo…
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## Description
When I use `sq.pl.ligrec` after `sq.gr.ligrec(
adata,
n_perms=100,
cluster_key="cluster",
clusters=["Polydendrocytes", "Oligodendrocytes"],
)
`, it always …
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[`models.qa_metric.LocalPairwise`](https://python-modelcif.readthedocs.io/en/latest/qa_metric.html#modelcif.qa_metric.LocalPairwise) is defined on the per-residue level, but as @arogozhnikov explaine…
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Hi, it appears the data for the protein-ligand docking is not on Hugging Face. Please advise on how to obtain this.
https://huggingface.co/microsoft/Graphormer/tree/main/Distributional-Graphormer/…
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Hi,
I want to dock a cofactor-substrate pair into several designed enzyme pocket (no metal). What I found was that the cofactor usually get a good pose while the substrate not. So I'm wondering:
…
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Hi,
For sequence dataset `from pinder.core.index.utils import get_sequence_database`, it has pdb_kind column with following types:
- ligand
- receptor
- dimer
- monomer
- predicted
How c…
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I want to randomize the starting pose of my ligand to remove bias from the initial pose, but it seems that the original conformation is still included when I run the following lines. Is there an error…
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Definitely not a big issue, mostly opening it because @mattwthompson told me to raise these issues 😅
**Description**
Passing an uncharged Molecule through `charge_from_molecule` leads to a Type…
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could you provide the list of proteins that have zinc-binding sites based on UniProt?
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I wanted to loop over families to extract ligands and interactions for each ligand, but when i run ligand.interactions() i get a KeyError. Even the example code presented on the GitHub page does not w…