How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations

The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of macromolecular structures and dynamics. As increasingly larger macromolecular systems are being studied, dimensionality effects such as the "curse of dimensionality" (a diminishing ability to discriminate pairwise differences between conformations with increasing system size) may exist and significantly impact RMSD-based analyses. For such large bimolecular systems, whether the RMSD or other alternative similarity measures might suffer from this "curse" and lose the ability to discriminate different macromolecular structures had not been explicitly addressed. Here, we show such dimensionality effects for both weighted and…

• NS
  National Science Council
• AS
  Academia Sinica