Highlights•The intrinsic dynamics, encoded in proteins' sequences and structures, are
utilized by stimuli to trigger allosteric and functional actions.•The modes of allosteric actions …

The spatial and temporal coordination of protein transport is an essential cornerstone of the
bacterial adaptation to different environmental conditions. By adjusting the protein …

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 …

Highlights•Hybrid methods of three kinds combine normal mode analysis and MD
simulations•Normal mode (NM)-driven simulations use NMs to enhance energy landscape …

Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a
challenge, especially when the extent and direction of the conformational changes taking …

The ribosome is a macromolecular complex which is responsible for protein synthesis in all
living cells according to their transcribed genetic information. Using X-ray crystallography …

Efficient sampling of conformational space is essential for elucidating functional/allosteric
mechanisms of proteins and generating ensembles of conformers for docking applications …

Trigger factor (TF) is a key component of the prokaryotic chaperone network, which is
involved in many basic cellular processes, such as protein folding, protein trafficking, and …