The kinetics of biomolecular isomerization processes, such as protein folding, is governed
by a free-energy surface of high dimensionality and complexity. As an alternative to …

In the presence of ATP, kinesin proceeds along the protofilament of microtubule by
alternated binding of two motor domains on the tubulin binding sites. Because the …

Multiscale methods are becoming increasingly promising as a way to characterize the
dynamics of large protein systems on biologically relevant time‐scales. The underlying …

Characterization of the structures of the transition state ensemble is a key step in describing
the folding reaction. Using two variants of a coarse-grained model of the three-stranded β …

The analysis of molecular motion starting from extensive sampling of molecular
configurations remains an important and challenging task in computational biology. Existing …

Protein structure prediction codes based on the associative memory Hamiltonian were used
to probe the binding modes between the nuclear localization signal (NLS) polypeptide of NF …

We study the folding thermodynamics and kinetics of the Pin1 WW domain, a three-stranded
β-sheet protein, by using all-atom (except nonpolar hydrogens) discontinuous molecular …

The measurement of distance between two objects is generalized to the case where the
objects are no longer points but are one-dimensional. Additional concepts such as …

Understanding the main stable shapes and transitions of biomolecules is key to solving
problems in computational biology. Because simulated molecular samples are high …

Abstract The NF-κB/IκB system provides a challenge to the structure-function paradigm since
both binding partners are partially disordered in the monomeric form. The experimental …