With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated
fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell …

As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …

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 …

We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and
free energy methods in Amber18. Of particular interest is the development of alchemical free …

Activation of the μ-opioid receptor (μOR) is responsible for the efficacy of the most effective
analgesics. To shed light on the structural basis for μOR activation, here we report a 2.1 Å X …

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …