Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …

We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …

Membrane permeability is a significant obstacle facing the development of cyclic peptide
drugs. However, membrane permeation mechanisms are poorly understood. To investigate …

Permeation of many small molecules through lipid bilayers can be directly observed in
molecular dynamics simulations on the nano-and microsecond timescale. While unbiased …

Predicting from first-principles the rate of passive permeation of small molecules across the
biological membrane represents a promising strategy for screening lead compounds …

Permeability (P m) across biological membranes is of fundamental importance and a key
factor in drug absorption, distribution, and development. Although the majority of drugs will …

Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of
biomolecular motions in atomistic resolution. However, the high computational demand of …

Umbrella sampling molecular dynamics simulations are widely used to enhance sampling
along the reaction coordinates of chemical reactions. The effect of the artificial bias can be …

A variety of enhanced statistical and numerical methods are now routinely used to extract
important thermodynamic and kinetic information from the vast amount of complex, high …

The free-energy profile of a compound is an essential measurement in evaluating the
membrane permeation process by means of theoretical methods. Computationally …