Molecular dynamics (MD) simulations are a key computational chemistry technique that
provide dynamic insight into the underlying atomic-level processes in the system under …

With recent advances in structural biology, including experimental techniques and deep
learning-enabled high-precision structure predictions, molecular dynamics methods that …

Computational modeling of assembly is challenging for many systems, because their
timescales can vastly exceed those accessible to simulations. This article describes the …

Proteins display a wealth of dynamical motions that can be probed using both experiments
and simulations. We present an approach to integrate side-chain NMR relaxation …

The increasing interest in modeling the dynamics of ever larger proteins has revealed a
fundamental problem with models that describe the molecular system as being in a global …

A novel approach to simulate simple protein–ligand systems at large time and length scales
is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction …

A varying number of particles is one of the most relevant characteristics of systems of interest
in nature and technology; ranging from the exchange of energy and matter with the …

Photoswitchable molecules can control the activity and functions of biomolecules by
triggering conformational changes. However, it is still challenging to fully understand such …

The evolutionary role of conformational exchange in the emergence and preservation of
function within structural homologs remains elusive. While protein engineering has revealed …

Machine learning (ML) has emerged as a pervasive tool in science, engineering, and
beyond. Its success has also led to several synergies with molecular dynamics (MD) …