We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …

Simulating protein folding has been a challenging problem for decades due to the long
timescales involved (compared with what is possible to simulate) and the challenges of …

It has become common to reference “pi-stacking” forces or “pi–pi interactions” when
describing the interactions between neighbouring aromatic rings. Here, we review …

We present the latest version of the Groningen Molecular Simulation program package,
GROMOS05. It has been developed for the dynamical modelling of (bio) molecules using …

A new implicit solvation model for use in Monte Carlo simulations of polypeptides is
introduced. The model is termed ABSINTH for self‐Assembly of Biomolecules Studied by an …

The efficient and accurate characterization of solvent effects is a key element in the
theoretical and computational study of biological problems. Implicit solvent models …

Visualizing the navigation of an ensemble of unfolded molecules through the bumpy energy
landscape in search of the native state gives a pictorial view of biomolecular folding. This …

Glucansucrases are large enzymes belonging to glycoside hydrolase family 70, which
catalyze the cleavage of sucrose into fructose and glucose, with the concomitant transfer of …

Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to
study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl …

Both turn sequence and interstrand hydrophobic side-chain–side-chain interaction have
been suggested to be important determinants of β-hairpin stability. However, their roles in …