I'm currently working on a GPCR and I need to model its N-terminal residues which are missing in its PDB structure. I need to have the correctly modeled N-terminus because I need to check its action. I have already found the best template for homology modeling but its PDB structure too does not have N-terminal residues.
Can you please help me to find a way to model N-Terminus of the GPCR?
Try chimera software
chimera-tools-structure editing- model/refined loop.
I just copy here the answer I gave you in your other post:
Hi there,
You can start by trying homology-based modelling. I find the SWISS-Model tool from expasy particularly interesting for this task:
https://swissmodel.expasy.org/
Another option is to go for Alphafold and, try to run a prediction:
https://alphafold.ebi.ac.uk/
However, take into account that the N-terminus of a GPCR could harbor a significant degree of disorder, so it could be hard to define the "exact secondary structure" (IDPs and so on...). I think that the following paper could be interesting for you in this regard:
Article Functional characterization of G-Protein Coupled receptors: ...
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