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Extending protein search for many proteins vs. many other proteins. Visualized with a hypergraph.

TODO

• Experiment
  • Use foldseek in python
  • Visualize a graph of the proteins
  • Select group on click
  • Query PDB for the clicked group
  • Parse the output graph with paper, bio data, structure from PDB
  • Use Graph RAG on the structures and paper to come up with function hypotheses (by Monday)
• Create user interface for anyone to use this process (By next Friday)
• Write the paper (By next Monday)

Development

Install the foldseek executable based on your system from https://github.com/steineggerlab/foldseek directly into the exec/ folder. Or if you have it installed globally, you can change the executable path config option (TODO). This is just so we can call Foldseek from Python.

References

• https://github.com/steineggerlab/foldseek
• https://venome.cqls.oregonstate.edu/proteins
• https://github.com/upphiminn/jLouvain