Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Comparing geometric and kinetic cluster algorithms for molecular simulation data

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Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

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Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Exploring the Universe of Protein Structures beyond the Protein Data Bank

(2010) Pilar Cossio et al.   PLoS Computational Biology

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B