RMSD: Routine measure stirs doubts

COMP 170

Jeremy J Yang, jj@eyesopen.com, OpenEye Scientific Software, 3600 Cerrillos Road, Suite 1107, Santa Fe, NM 87507
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.

Poster Session -- Sponsored by Novartis Institutes for BioMedical Research
6:00 PM-8:00 PM, Tuesday, 30 August 2005 Washington DC Convention Center -- Hall A, Poster

8:00 PM-10:00 PM, Monday, 29 August 2005 Washington DC Convention Center -- Hall A, Sci-Mix

Division of Computers in Chemistry

The 230th ACS National Meeting, in Washington, DC, Aug 28-Sept 1, 2005