SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding
domain (RBD), which transitions from a glycan-shielded 'down'to an exposed 'up'state to …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Protein switches perform essential roles in many biological processes and are exciting
targets for de novo protein design, which aims to produce proteins of arbitrary shape and …

Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for
lifestyle transitions, such as cell proliferation or apoptosis, switch-like characteristics are …

Highlights•Designing genetically encoded fluorescence-based analyte biosensors is not
trivial.•Many current design efforts take a nature-inspired, modular approach.•Individual …

A grand challenge in the field of biophysics has been the complete characterization of
protein–protein binding processes at atomic resolution. This characterization requires the …

Allostery enables proteins to interconvert different biochemical signals and form complex
metabolic and signaling networks. We hypothesize that circular permutation of proteins …

A promising approach for simulating rare events with rigorous kinetics is the weighted
ensemble path sampling strategy. One challenge of this strategy is the division of …

The natural function of many proteins depends on their ability to switch their conformation
driven by environmental changes. In this work, we present a small, monomeric β-sheet …

Weighted ensemble (WE) is an enhanced sampling method based on periodically
replicating and pruning trajectories generated in parallel. WE has grown increasingly …