The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …

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 …

Highlights•Coarse-grained models are reduced representations of all-atom models that aim
to retain the essential molecular aspects for the system of interest.•Coarse-grained …

Drug discovery is the process used to discover new candidate medications. In the past, most
drugs were discovered by identification of active-ingredients or by serendipity. Modern drug …

Protein conformational changes are at the heart of cell functions, from signalling to ion
transport. However, the transient nature of the intermediates along transition pathways …

Highlights•Discrete Molecular Dynamics (DMD) accelerates simulation of large
biomolecules.•Increased sampling over MD allows microsecond simulations on a personal …

Diverse classes of proteins function through large-scale conformational changes and
various sophisticated computational algorithms have been proposed to enhance sampling …

There is a variety of experimental and computational techniques available to explore protein
dynamics, each presenting advantages and limitations. One promising experimental …