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I think we can find a published list of some proteins with large conformational changes and spin off simulations of these and run through the analysis. Correlations between angles with large direction…
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**Is your feature request related to a problem? Please describe.**
Please provide documentation on the submission for GlycoProteins for 3D structure generation. The input would be a PDB ID for the pr…
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Hi @nslavov ,
Thank you very much for your contribution regarding the single-cell protein data. I believe it will be of great assistance to my research. I am a Ph.D. candidate in bioinformatics, and…
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I installed localcolabfold and copied HighFold git repo into my localcolabfold.
So that my localcolabfold git repo looks as
![Screenshot 2024-06-25 at 5 29 04 PM](https://github.com/hongliangduan/…
kimdn updated
2 months ago
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Please check that the term does not already exist by using the ontology search tool OLS:
https://www.ebi.ac.uk/ols4/ontologies/cl
**Preferred term label**
Lamina propria fibroblast (S1)
**Sy…
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**Command that I ran:**
```
asap-ml build-dataset schnet --exp-file unknown_error.json \
--structures '*_complex.pdb' \
--ds-cache ~/dataset_cache_local.pkl \
--xtal-regex '(?
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We should switch to openMM for minimization after structural models have been built.
- Need to minimize structures with small molecules bound
- Want to score structures with both protein+ligand …
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Hi,
As searching for protein-protein interactions, my aim was to find similar interfaces in the PDB with Foldseek-multimer. I thought it would only return hits where the two similar chains are in i…
gezmi updated
4 months ago
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We added a nmdc schema Class for the gene aggregation for the sequencing workflows, see https://microbiomedata.github.io/nmdc-schema/FunctionalAnnotationAggMember/, but not for the metaproteomics. I b…
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Hello ! I'm still new to learning on proteins and I was wondering how to train on the Structure Similarity Task (at least in an efficient manner) when using the graph format for PyTorch Geometric.
…