Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator)
contain the essential information about the molecular thermodynamics and kinetics. This …

Free-energy calculations have seen increased usage in structure-based drug design. Despite
the rising interest, automation of the complex calculations and subsequent analysis of …

The study of folding and conformational changes of macromolecules by molecular dynamics
simulations often requires the generation of large amounts of simulation data that are …

We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing
configuration-space-discretized simulation trajectories produced at different thermodynamic …

Computing the equilibrium properties of complex systems, such as free energy differences, is
often hampered by rare events in the dynamics. Enhanced sampling methods may be used …

Molecular-dynamics simulations are increasingly used to study dynamic properties of
biological systems. With this development, the ability of force fields to successfully predict …

Free energy calculations are rapidly becoming indispensable in structure-enabled drug
discovery programs. As new methods, force fields, and implementations are developed, …

We explore the dynamical large deviations of a lattice heteropolymer model of a protein by
means of path sampling of trajectories. We uncover the existence of nonequilibrium …

Accurate in silico prediction of protein–ligand binding affinity is important in the early stages
of drug discovery. Deep learning-based methods exist but have yet to overtake more …