Abstract Active matter, responsive (“smart”) materials and materials under time-dependent
load are systems out of thermal equilibrium. To construct coarse-grained models for such …

The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …

Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …

Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

Enhanced sampling techniques have traditionally encountered two significant challenges:
identifying suitable reaction coordinates and addressing the exploration–exploitation …

Markov state models (MSMs) have been widely applied to study the kinetics and pathways
of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) …

Biomolecular dynamics play an important role in numerous biological processes. Markov
State Models (MSMs) provide a powerful approach to study these dynamic processes by …

Targeted protein degradation (TPD) is emerging as a promising therapeutic approach for
cancer and other diseases, with an increasing number of programs demonstrating its …

The generalized master equation (GME) provides a powerful approach to study
biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics …

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