Hi I had modelled a heptamer transmembrane protein missing 10-residues within the extracellular loops via MODELLER constraining the known residues as a heptamer (when MODELLER modeled as a monomer and the Galaxyweb oligomerized the result exhibited too high of an RMSD). Accordingly the result of a screenshot is attached below exhibiting these highly-dynamic loop-regions (one -in-red) repelling each other possibly intentionally via MODELLER would you agree? (I ask since Alphafold modeled just one monomer which did not exhibit this repulsion, also see in attached screenshot in yellow.) If you would recommend the non-repulsion Alphafold model then I would have the choice to excise the modeled loop-region and splice it into the experimentally proven Cryo-EM PDB Databased model.
Thanks if you have any input and interaction from the loops, to my knowledge, would only be via residue interactions i.e. charges, hydrophobs etc. not towards ligand interactions.
Best,
Joel 🚀
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