All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …

Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the
long, costly process of bringing a new medicine to patients. For example, the time a drug …

The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …

Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW
domain, was simulated via accelerated molecular dynamics (aMD). In comparison with …

Free energy calculations are central to understanding the structure, dynamics and function
of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded …