Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …

Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …

The study of the rare transitions that take place between long lived metastable states is a
major challenge in molecular dynamics simulations. Many of the methods suggested to …

Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …

Cyclic peptides extend the druggable target space due to their size, flexibility, and hydrogen-
bonding capacity. However, these properties impact also their passive membrane …

This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …

The function of light-harvesting complexes is determined by a complex network of dynamic
interactions among all the different components: the aggregate of pigments, the protein, and …

Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular
dynamics (MD) simulations are an invaluable tool to study conformational changes in …

Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …