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 …

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 …

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 …

In recent years, there has been a surge in the number of studies exploring the relationship
between proteins' equilibrium dynamics and structural changes involved in function. An …

Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an
effective antiviral drug nor a vaccine against SARS is available. However, it was found that a …

Although tetracyclines are an important class of antibiotics for use in agriculture and the
clinic, their efficacy is threatened by increasing resistance. Resistance to tetracyclines can …

The stimulator-of-interferon-genes (STING) protein is involved in innate immunity. It has
recently been shown that modulation of STING can lead to an aggressive antitumor …

Owing to their plasticity, intrinsically disordered and multidomain proteins require
descriptions based on multiple conformations, thus calling for techniques and analysis tools …

Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple
life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV …