Protein dynamics by NMR has been reviewed extensively in recent years [1–10]. These
surveys show decisively that information on structure should be complemented by …

Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a
variety of bead types and sizes with a new mapping approach, the newest version of the …

Background Many proteins undergo extensive conformational changes as part of their
functionality. Tracing these changes is important for understanding the way these proteins …

We describe a new method for rapidly generating stereochemically acceptable pathways in
proteins. The method, called geometric targeting, is publicly available at the webserver …

Accurate sampling of conformational space and, in particular, the transitions between
functional substates has been a challenge in molecular dynamic (MD) simulations of large …

Background Obtaining atomic-scale information about large-amplitude conformational
transitions in proteins is a challenging problem for both experimental and computational …

Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of
their evolutionary selection in carrying out their biological functions. Although the dynamics …

A fundamental problem in computational biophysics is to deduce the function of a protein
from the structure. Many biological macromolecules such as enzymes, molecular motors or …

The elastic network (EN) is a prime model that describes the long-time dynamics of
biomolecules. However, the use of harmonic potentials renders this model insufficient for …

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for
proteins undergoing large conformational changes. In the absence of bound structures …