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
If you need additional help, please email us at help@schrodinger.com.
Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles