Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …

Advances in DNA sequencing and machine learning are providing insights into protein
sequences and structures on an enormous scale. However, the energetics driving folding …

Proteins fold into unique native structures stabilized by thousands of weak interactions that
collectively overcome the entropic cost of folding. Although these forces are “encoded” in the …

An outstanding challenge in the field of molecular biology has been to understand the
process by which proteins fold into their characteristic three-dimensional structures. Here …

The millisecond time scale needed for molecular dynamics simulations to approach the
quantitative study of protein folding is not yet routine. One approach to extend the simulation …

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a
lower cost scaling than the prevailing Kohn–Sham DFT, which is increasingly desired for …

The studies of the folding of structurally related proteins have proved to be a very important
tool for investigating protein folding. Here we review some of the insights that have been …

We introduce Gaussian accelerated MELD (GaMELD) as a new method for exploring the
energy landscape of biomolecules. GaMELD combines the strengths of Gaussian …

Single-molecule fluorescence resonance energy transfer (smFRET) experiments are
extremely useful in studying protein folding but are generally limited to time scales of greater …

Molecular Biology of Assemblies and Machines provides a comprehensive narrative of the
ways in which macromolecular structures assemble and how they interact with other …