Skip to content

Latest commit

 

History

History
29 lines (19 loc) · 1.05 KB

README.md

File metadata and controls

29 lines (19 loc) · 1.05 KB
Raw

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