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The current version of MoleculeNet has the PDBBind Protein-ligand collection benchmarked. It would be nice to add the Protein-Protein PDBBind collection and the Protein-Nucleic Acid collections (also …
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There are 16 new proteins measured in plasma
There is also a list of 42 existing terms measured in blood serum, but for this paper, all the proteins are measured in plasma. I added these to Excel.
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See line _1392_ as example,
`atom._coords = [ [ float(rec[5]), float(rec[6]), float(rec[7]) ] ]`
the `rec` here comes from line _1308_:
`rec = split(rec)`
Sometimes protein PDB file content looks…
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**Please describe your question, idea, or concern.**
Dear GO team,
I have a question about the 'Date' field in GAF files. While looking through human GAF files (goa_human.gaf downloaded from GO Da…
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First, thanks so much for this fantastic tool
I was analyzing a collection of plasmids from pseudomonads, and came across predictions of relaxases that were unexpected, because I got a prediction w…
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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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Good morning,
I would like to propose you to share another extremely useful example of AF2 usage. Many scientists are using protein embeddings for downstream tasks (i.e. function prediction). [AF2 …
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Hello,
I am trying to run the example code to predict protein monomer 7u7w_A and I get the following error
`./SE3nv-20240131.sif -m rf2aa.run_inference --config-name protein
/usr/lib/python3.10/…
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We should have a way to represent Protein Ambiguity Groups in mzTab. My
suggestions is that we can add an optional columns with the CVterm MS:1001591
which is the anchor protein. If we use this …