When creating an alignment between 2 proteins in PyMOL, should I use the RMSD or Match Align Score to determine if the 2 structures are similar?
Hi Jessica,
I haven't seen many people quoting the Match Align Score, so I think it makes more sense to use the RMSD to describe how well the proteins match. I often use the RMSD of just the backbone atoms since there is always some imperfections in the side chains that don't have anything to do with the similarity of the proteins.
I also recommend the Matchmaker tool in Chimera software for this. I think it is more user friendly and can create sequence aligments for each structural alignment.
Using RMSD to depict alignment is a standard practice. RMSD value under 3 Å is considered acceptable in most cases.
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