Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Atomistic or ab initio molecular dynamics simulations are widely used to predict
thermodynamics and kinetics and relate them to molecular structure. A common approach to …

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 …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …

Inspired by the success of deep learning techniques in the physical and chemical sciences,
we apply a modification of an autoencoder type deep neural network to the task of …

Protein–protein association is fundamental to many life processes. However, a microscopic
model describing the structures and kinetics during association and dissociation is lacking …

Recent advances in molecular simulations have allowed scientists to investigate slower
biological processes than ever before. Together with these advances came an explosion of …