It has recently become practical to construct Markov state models (MSMs) that reproduce
the long-time statistical conformational dynamics of biomolecules using data from molecular …

Improved rational drug design methods are needed to lower the cost and increase the
success rate of drug discovery and development. Alchemical binding free energy calculations, …

Recent calorimetric studies of interactions between small molecules and biomolecular targets
have generated renewed interest in the phenomenon of entropy-enthalpy compensation. …

We present a new estimator for computing free energy differences and thermodynamic
expectations as well as their uncertainties from samples obtained from multiple equilibrium states …

An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape 1 , 2 – 3 , have
activity against diverse sarbecoviruses 4 , 5 , 6 – 7 , and be highly protective through viral …

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …

Molecular force fields have been approaching a generational transition over the past several
years, moving away from well-established and well-tuned, but intrinsically limited, fixed …

Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics
of a molecule is approximated by a Markov chain on a discrete partition of configuration …

To meet the challenge of modeling the conformational dynamics of biological macromolecules
over long time scales, much recent effort has been devoted to constructing stochastic …

OpenMM is a software toolkit for performing molecular simulations on a range of high
performance computing architectures. It is based on a layered architecture: the lower layers …