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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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Hello!
I have a query concerning a specific aspect of protein-ligand systems. In cases where both the protein and ligand are identical, but the final conformation varies due to sampling of the protei…
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Hi, I have a corpus of about 500,000 protein sequences and would like to apply them to existing models like ESM2 or this one for predicting the fitness effect of changing an amino-acid for another.
H…
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Errors remaining:
error - a_study_protein-protein interaction detection_protein microarray.txt
Invalid ISA-TAB: unexpected field Derived Data File found in section transcriptomics_pipeline
warning -…
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Hi team,
I am trying to refine a Modeller-generated structure of a membrane dimeric protein with bound ligand. Is it going to be possible with PREFMD2?
Just want to ask since I see some hashed …
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Hi @kimrutherford @ValWood,
I was drafting the email to announce the changes, but I realised a few things that perhaps we should address:
* [x] A lot of "new genes" lacking references: both [pro…
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Hi David,
I ran into this amazing package, and since I'm more of a protein person, I was wondering if you could make something similar to represent protein domains and secondary structure.
L…
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#### Current behavior:
26 genes are discovered to be uncorrelated with their corresponding reactions in `Glycosphingolipid metabolism` and `Glycosylphosphatidylinositol (GPI)-anchor biosynthesi…
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Should be straightforward. Need to think about file format.
This should be split into 3 files.
* 1 file should have disorder and disorder score from disopred (for disorder_res and disordScore_r…
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I am trying to test this model on some new antigens.
In con_pdb_dict_AgAb.pickle there are three versions of data, of sizes 3, 46, 66 respectively.
Could you add some documents on these features…