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Hello,
Is there a way to extract the MCL graph edge weights between pairs of proteins that have been declared as orthologues?
As far as I can tell, the OrthoFinder_graph.txt file should have the…
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As a result of the GO-CAM specs call today, we made the decision that cellular anatomical structures represent a location in GO. Gene products and complexes will be located in those anatomical structu…
ukemi updated
2 years ago
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Hello Ziqi, we have some issues about the data processing for new datasets.
1) We used ID in ensp_uniprot.txt to download native protein structures, but we discovered that over 600 native protein st…
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We have a list of possible visualisations in the `visualisations.ipynb` notebook (in the examples folder), but @rhoslynroebuck found that some of these may not be working correctly. This may be a non-…
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> http://dx.doi.org/10.1371/journal.pone.0141287
>
> **Motivation:** We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to…
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Dear team,
Thank you very much for providing Open-ComBind as a command-line tool for docking pose selection. I have results from a previous docking job using GNINA with CNN-scoring. I have 10 prote…
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Hi, how to deal with a system containing metals？
And the protonation state of the atoms chelated with metals?
Also, how to relax water?
Thank you!
[7xrl](https://www.rcsb.org/structure/7xrl) a…
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This is a popular representation for bio-molecules, in particular proteins, supported by both JSmol and 3Dmol.js. Two separate people asked for us to support this!
This kind of representation requi…
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In some cases we have incomplete cliques that are chemicals and proteins:
- https://github.com/TranslatorSRI/Babel/issues/200
- https://github.com/TranslatorSRI/Babel/issues/232
- https://github.co…