G. Will, N. Masciocchi, et al.
Zeitschrift fur Kristallographie - New Crystal Structures
The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF̄). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as "intermediates" or well-defined stable states. © 2014 American Chemical Society.
G. Will, N. Masciocchi, et al.
Zeitschrift fur Kristallographie - New Crystal Structures
A. Gangulee, F.M. D'Heurle
Thin Solid Films
Shaoning Yao, Wei-Tsu Tseng, et al.
ADMETA 2011
Douglass S. Kalika, David W. Giles, et al.
Journal of Rheology