I wanted to ask if I can use structure of an intrinsically disordered protein modelled via Alphafold Colab directory if I can use this model further for studying post translational modification via Vienna PTM and then subsequent molecular dynamics simulation.
You can certainly try this if it really works is another question. One thing you can check is if the regions that are known to be Disordered have low score. pLDDT < 50 was associated with Disordered proteins in the original EMBL publication and so this could be used as disorder indicator.
Regarding post translational modifications I think the process itself you can not model (highly unsure about that) but if you are able to generate a modified version of the protein you can of course do a MD afterwards.
I would search the literature for that more (a short search basically only yielded post translational modification predictors nothing really about dynamics).
This is not really an answer but hopefully still a somewhat useful comment.
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Graphs