Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …

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 …

Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly
challenging to predict computationally and, therefore, is usually not considered in the early …

Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of
the most effective ways to solve the problem of fossil resource shortage, energy security, and …

Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the
advent of computers, many scientists have put efforts in developing theoretical models that …

Highlights•A public–private partnership targets drug-binding kinetics in a multilevel
approach.•New experimental approaches for measuring drug residence time are …

Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …

Drug action is inherently multiscale: it connects molecular interactions to emergent
properties at cellular and larger scales. Simulation techniques at each of these different …