The calculation of free‐energy differences is one of the main challenges in computational
biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of …

In recent years, the fabrication of nanomaterials and exploration of their properties have
attracted the attention of all branches of science, such as physics, chemistry, biology, and …

Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the
advent of computers, many scientists have put efforts in developing theoretical models that …

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 …

The metadynamics or hills method is a relatively new molecular dynamics technique aimed
to enhance the sampling of separated regions in phase space and map out the underlying …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

" Extended Ensemble Monte Carlo" is a generic term that indicates a set of algorithms, which
are now popular in a variety of fields in physics and statistical information processing …

Proteins are dynamic molecules that can transition between a potentially wide range of
structures comprising their conformational ensemble. The nature of these conformations and …

The efficiencies of two recently developed methods for calculating free energy changes
along a generalized coordinate in a system are discussed in the context of other, related …

Optimal free energy paths (OFEPs) for conformational transitions are parallel to the mean
force at every nonstationary point of the free energy landscape. In contrast to adiabatic …