Title:

RMSD - Routine measure stirs doubts

Author:

Jeremy Yang
OpenEye

Abstract:

Root mean square distance (RMSD) measurements between molecule
conformations are routine and widespread in scientific literature.
It appears widely accepted that to measure the difference or sameness
between conformers, that is, a distance in "conformation space", a
sole RMSD calculation is sufficient.  While some interaction models
depend on the square of interatomic distance, does this provide a
physical basis for use of RMSD?  Is the current widespread use of RMSD
justified, and if so how?  This study examines and evaluates RMSD and
its uses, and some alternative measures of distance between
conformers.