The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …

A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

The realization that experimentally observed functional motions of proteins can be predicted
by coarse-grained normal mode analysis has renewed interest in applications to structural …

Several molecular dynamics (MD) simulations were used to sample conformations in the
neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories …

Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques,
we provide a novel method to explore all-atom energy landscapes. The core of the …

Background Normal mode analysis (NMA) using elastic network models is a reliable and
cost-effective computational method to characterise protein flexibility and by extension, their …

Highlights•Intrinsic dynamics plays a major role in enabling protein interactions.•Soft/global
modes of motions facilitate binding and assembly.•Soft modes define pre-existing pathways …

Motivation: The function of a protein depends not only on its structure but also on its
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …

Publisher Summary This chapter discusses the need for multivariate analysis in biophysical
studies, presents the way principal components analysis (PCA) can be implemented in the …

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their
most cooperative fluctuations accessible under native state conditions, is a first step towards …