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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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We need to provide instructions to Robel to deal with the following issue:
OGlcNAc MCW source files have rows with sites in this format: "T291 (P05067-4);T292 (P05067-4);T576 (P05067-4)"
The QC sc…
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I am trying to link a registered sample (protein) as an (optional) attribute (called protein_id) in a sample (genetic part) that I extract from a datafile.
**Behavior1**
If I leave the registered s…
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[Asset 595](https://github.com/NCATSTranslator/Tests/blob/main/test_assets/Asset_595.json) currently uses [UMLS:C0040018](https://nodenormalization-sri.renci.org/get_normalized_nodes?curie=UMLS:C00400…
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Hi,
I setup the github repository in my location machine (Ubuntu 22) by cloning the repository and following the instructions in the README file.
After which, I rand the code with the example fi…
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We had some questions concerning variables the modelling of variables where the property is in relation to some kind of reference point. Take [Root mean square deviation of atomic positions](https://e…
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### Issue summary
Hi,
I am wondering if water molecules in a protein pdb file would be sampled during gnina docking process, with refinement used only in the rescore level and not whole protein do…
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When running the modelBasedQCPlots function, the output is missing the protein names in the title, so eg instead of "Normal Q−Q Plot ( A2AAJ9 )" it now says "Normal Q−Q Plot ( )". The plots themselves…
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Hi,
@GitteDecatBIT is working on a new adapter for Biocypher -
it would be an adapter for the consolidated protein-protein interaction dataset [iRefindex](https://irefindex.vib.be).
The adapt…
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@DaniallMasood ... why do the protein components have the same "Biomarker" and "Assessed Biomarker Entity" values as the glycan components?