By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

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 …

It has become commonplace to employ principal component analysis to reveal the most
important motions in proteins. This method is more commonly known by its acronym, PCA …

Enzymes are the natural catalysts that execute biochemical reactions upholding life. Their
natural effectiveness has been fine-tuned as a result of millions of years of natural evolution …

Allosteric transition, defined as conformational changes induced by ligand binding, is one of
the fundamental properties of proteins. Allostery has been observed and characterized in …

Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …

Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …

Abstract The interface of protein structural biology, protein biophysics, molecular evolution,
and molecular population genetics forms the foundations for a mechanistic understanding of …

We present the first microsecond MD simulation of B-DNA. Trajectory shows good
agreement with available data and clarifies the μs dynamics of DNA. The duplex is sampling …