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Article ID: 156 - Last Modified: December 4, 2010

The "align GPCR" mode in Prime gives me a poor alignment for helix 5 in my class A GPCR. Why is this?

Helix 5 is notoriously difficult to align, even when using the known conserved sequence motifs. This is due to the fact that even the helix 5 motifs are not that well conserved. The best approach in this case is to use the Multiple Sequence Viewer to generate a multiple sequence alignment to help guide the alignment of this helix.

Keywords: Prime, GPCR, Homology Model, Sequence Alignment, Maestro

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