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It looks like the script doesn't work when running on predictions that have modified residues. For example, running on a prediction that contains several Aceytyl-Lysine (three letter code "ALY") resid…
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- [ ] add a legend
- [x] set a consistent color scale across all time points, so they are comparable
- [ ] make color gradient customizable, to fix dynamic range
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decreased protein localization to cell surface
decreased protein localization to cell surface with increased localization to endosomal structures
decreased protein localization to cell surface, misl…
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Hi Team,
Thank you for the excellent work on ESM3.
I am currently comparing the performance of ESM3 on the CAMEO and CASP14 datasets with ESMFold and AlphaFold2. The CAMEO dataset I am using is …
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In the issue mentioned in the UAMMD repository (https://github.com/RaulPPelaez/UAMMD/issues/38), I followed your advice to modify the JSON file and attempted to remove the extra forces, but the system…
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Hi @Elcock-Lab
Thanks for such a wonderful paper and novel insights based on AF structures. I have a few queries about the code:
**Query1:** In the paper you said
>To prevent the counting of t…
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Hi,
I'm new to foldseek and I wonder if you can you provide guidance on how I can obtain structure alignment of a small fragment of a protein. Basically, the protein has a 8-aa forming a beta-hairpin…
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Add protein structure descriptors as structure-level feature sets that can be pre-loaded.
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Figured I should start a thread of what the pseudocode might look like for this repo, and what sort of user facing stuff might look like.
Here's a quick 5-minute attempt at what the pipeline would…
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Hello,
I am encountering an issue when using molpc2 to predict the structure of large proteins with known stoichiometry information. For example, when I try to predict the structure of 1A8R (or 5BSE)…