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starbeachlab / MutationExplorerServer

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Entering single amino acid deletions? #17

Open navinbr opened 4 days ago

navinbr commented 4 days ago

Hi, I wondered if it's possible to enter single amino acid deletions like 222del for instance? (It so happens the mutations ended up being 3bp deletions). Or if you happen to know what software I should use instead for this, that would be great! Thank you for any tips.

renedominik commented 3 days ago

Hi, currently only variations/mutations are possible using the MutationExplorer. Insertions and deletions involve a rearrangement of the backbone conformation, which is computationally too expensive for a webservice. It can be achieved using Molecular Dynamics or Rosetta. Probably also with other methods. Both paths will not be simple, I assume. If the position is located in a loop, I would go for Rosetta's loop modelling application.

navinbr commented 3 days ago

Thank you for the tips. I did Alphafold3 (explored the pLDDTs and PAEs which may already be interesting), then followed by foldX repair, then I compared the dGs. If anything strikes you here as incorrect do let me know. But I will also look into Rosetta - thank you!

renedominik commented 3 days ago

Sounds great, straightforward and not limited to loop positions. You could check with MD or Rosetta whether the structures could be further refined.