In the last decades biomolecular simulation has made tremendous inroads to help elucidate
biomolecular processes in-silico. Despite enormous advances in molecular dynamics …

The detailed characterization of the overall free energy landscape associated with the
folding process of a protein is the ultimate goal in protein folding studies. Modern …

Characterizing the equilibrium ensemble of folding pathways, including their relative
probability, is one of the major challenges in protein folding theory today. Although this …

Highlights•Advances, common features, and remaining challenges are presented for path
sampling approaches.•Key strengths are the efficient calculation of transition trajectories and …

Dimensionality reduction with a suitable choice of order parameters or reaction coordinates
is commonly used for analyzing high-dimensional time-series data generated by atomistic …

Proteins often undergo slow structural rearrangements that involve several angstroms and
surpass the nanosecond timescale. These spatiotemporal scales challenge physics-based …

This review discusses successful strategies and key open problems in the kinetic and
thermodynamic characterization of complex biomolecular systems by computer simulations …

The structure of proteins has long been recognized to hold the key to understanding and
engineering their function, and rapid advances in structural biology and protein structure …

Conformational transitions are essential for the functioning of many proteins, and
understanding this dynamical behavior is a central goal in molecular biology. Computer …

Atomistic simulations can provide valuable, experimentally-verifiable insights into protein
folding mechanisms, but existing ab initio simulation methods are restricted to only the …