Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure
predictions for molecular systems of medium and large size. Jaguar focuses on …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

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 …

Designing tight-binding ligands is a primary objective of small-molecule drug discovery.
Over the past few decades, free-energy calculations have benefited from improved force …

Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

α-Synuclein (α-syn) phosphorylation at serine 129 (pS129–α-syn) is substantially increased
in Lewy body disease, such as Parkinson's disease (PD) and dementia with Lewy bodies …

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 …

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 …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …