Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

An increasing number of studies have reported computations of the standard (absolute)
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …

The ff94 force field that is commonly associated with the Amber simulation package is one of
the most widely used parameter sets for biomolecular simulation. After a decade of …

The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Molecular dynamics simulation methods produce trajectories of atomic positions (and
optionally velocities and energies) as a function of time and provide a representation of the …

The proper functioning of biomolecules in living cells requires them to assume particular
structures and to undergo conformational changes. Both biomolecular structure and motion …

Enzymes are very efficient catalysts that are essential for the functioning of living organisms.
The low efficiency of biocatalysts produced de novo relative to those that have evolved …

Biomolecular recognition can be stubborn; changes in the structures of associating
molecules, or the environments in which they associate, often yield compensating changes …

Proteins are not static but are flexible molecules that can adopt many different
conformations. The HIV-1 protease is an important target for the development of therapies to …