Q:
I have come across the Macromolecular Database and I
was curious to how a degree of motion is quantified in this site. In the
following link for one of the entries (HIV protease:
http://www.molmovdb.org/cgi-bin/motion.cgi?ID=hivprot), the third box from
the top entitled ‘Description’ says of HIV protease:

"Two large loop regions, that together comprise one quarter of the
structure, move CA atoms ~7 Angstroms"

Is this referring to a RMSD value of an ensemble of structures? Is this a
RMSD value of the whole protein, or only for the domain of those two large
loop regions?

A:
This is described in the DB paper
(http://papers.gersteinlab.org/papers/molmovdb2).