Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs
Fig 4
Examples of results obtainable with RosettaGPCR.
In all cases, the crystal structure is colored grey and the model is blue. Three different ECL2 loops structures are presented: disordered (A), β-sheet (B), and lipid-binding (C). RosettaGPCR performs well on loops containing the conserved disulfide. For lipid receptors lacking the conserved disulfide (C) multiple templates (blue) perform worse than using a single template with similar structure (green), in this case the LPA receptor. Extracellular loops 3 (D) and 1 (E) also perform quite well with this method. In general, RosettaGPCR can model the TM region of most receptors below 2 Å (F). However, for receptors like rhodopsin with complex loop structures and termini (red), the model (cyan) fails to capture the overall conformation (8.0 Å RMSD).