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- [ ] settings for concentration
- [ ] predefined mesh generation params
- [ ] settings for speeds
High, medium, low "realism" settings, or slider if possible, can change
- shape of mesh (complicated…
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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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These were so far created in separate scripts. Probably shouldn't be fully integrated with the training routines, but it would be good to add them in utils or somewhere similar so that users can crate…
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Usually when I click on the hyperlink for a protein family, it takes me to a table that allows me to see all the proteins across all the genomes that belong to this family.
When I click on t…
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Hello,
I am interested in molecular dynamic simulations for systems other than proteins/membranes, etc.
Specifically, I want to run simulations for system like carbon nanostructures or boron-ni…
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When testing the new protein chain grounding feature, I found something odd, namely, several synonyms that I confirmed to be listed in `uniprot-proteins.tsv.gz`, e.g., `Spike glycoprotein` were not re…
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Choose colors and icons, potentially create templates and enrich the detail panels for
Pathways, Proteins, Entities,
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So this maybe just an FYI for these entities: PATHGO_0000103 (host toll-like receptor signaling disruption factor) AND PATHGO_0000233 (disrupts host toll-like receptor signaling). This is related to i…
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**Bug description**
I installed esm using the conda environment
I Folded many proteins using the esm-fold command, however I have found some proteins with physically impossible structure.
**Rep…
em255 updated
11 months ago
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Hi Will,
Thanks for your time in advance:
I am trying to use Mokapot on sage results of timsTOF DDA data - nothing special. The issue I encounter is the following:
Mokapot on the pin file with…