Molecular dynamics (MD) has become increasingly popular due to the development of
hardware and software solutions and the improvement in algorithms, which allowed …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

The study of drug-receptor interactions has largely been framed in terms of the equilibrium
thermodynamic binding affinity, an in vitro measure of the stability of the drug-receptor …

Introduction For rational drug design, it is crucial to understand the receptor-drug binding
processes and mechanisms. A new era for the use of computer simulations in predicting …

We here report on nonequilibrium targeted molecular dynamics simulations as a tool for the
estimation of protein–ligand unbinding kinetics. Correlating simulations with experimental …

The possibility of using the atomic coordinates of protein-ligand complexes to assess
binding affinity has a beneficial impact in the early stages of drug development and design …

Molecular dynamics simulation is a widely employed computational technique for studying
the dynamic behavior of molecular systems over time. By simulating macromolecular …

Supervised MD (SuMD) is a computational method that enables the exploration of ligand–
receptor recognition pathway in a reduced timescale. The performance speedup is due to …

Ligand-protein binding models have experienced an evolution during time: from the lock-key
model to induced-fit and conformational selection, the role of protein flexibility has become …

Accurate prediction of protein‐ligand binding affinities is an essential challenge in structure‐
based drug design. Despite recent advances in data‐driven methods for affinity prediction …