Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …

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 …

We describe a new method for modeling protein and ligand main‐chain flexibility, and show
its ability to model flexible molecular recognition. The goal is to sample the full …

Allosteric proteins have been studied extensively in the last 40 years, but so far, no
systematic analysis of conformational changes between allosteric structures has been …

Biochemical activity and core stability are essential properties of proteins, maintained
usually by conserved amino acids. Structural dynamics emerged in recent years as another …

In this article we focus on presenting a broad range of examples illustrating low-energy
transitions via hinge-bending motions. The examples are divided according to the type of …

Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular
dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of …

Allosteric regulation in biological systems is of considerable interest given the vast number
of proteins that exhibit such behavior. Network models obtained from molecular dynamics …

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 …