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Opened 3 years ago
#8013 assigned enhancement
Compare alphafold database structure conformations for all sequences similar to a query
| Reported by: | Tom Goddard | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
It might be informative to see the different conformations AlphaFold (or ESMfold) predicts for all sequences similar to a query sequence. I could use the kmer-search (or BLAST) to find all AlphaFold database similar sequences, then align and cluster all the predicted structures and then show cluster representatives as sequence of models. Probably need to ignore the low confidence (disordered) regions when aligning and clustering. Could order the models by how close they are in structure. I would guess there might be up to hundreds of conformations.
This could be helpful in a few ways. It could indicate actual alternate conformations of a protein of interest. Or it could indicate uncertainty in the AlphaFold predictions.
It would also be useful to have a sequence alignment associated with this set of conformation representatives.
