With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Highlights•ENMs efficiently capture the collective functional motions of macromolecules.•The
intrinsic dynamics predictable by ENMs is robust to different coarse-grained …

Background Popular bioinformatics approaches for studying protein functional dynamics
include comparisons of crystallographic structures, molecular dynamics simulations and …

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 …

Normal mode analysis is a computational technique that allows to study the dynamics of
biological macromolecules. It was first applied to small protein cases, more than thirty years …

We present a new conceptually simple and computationally efficient method for nonlinear
normal-mode analysis called NOLB. It relies on the rotations-translations of blocks (RTB) …

Recent years have seen several hybrid simulation methods for exploring the conformational
space of proteins and their complexes or assemblies. These methods often combine fast …

Introduction Evolution and design of protein complexes are frequently viewed through the
lens of amino acid mutations at protein interfaces, but we showed previously that residues …

Abstract Background Elastic network models (ENMs) are based on the simple idea that a
protein can be described as a set of particles connected by springs, which can then be used …

Proteins in cellular environments are highly susceptible. Local perturbations to any residue
can be sensed by other spatially distal residues in the protein molecule, showing long-range …