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 …

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 …

The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron
spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) …

Background Molecular dynamics has emerged as an important research methodology
covering systems to the level of millions of atoms. However, insufficient sampling often limits …

Z-DNA duplexes are a particularly complicated test case for current force fields. We
performed a set of explicit solvent molecular dynamics (MD) simulations with various …

The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …

The quantitative assessment of uncertainty and sampling quality is essential in molecular
simulation. Many systems of interest are highly complex, often at the edge of current …

We develop a framework for the design of optimized alchemical transformation pathways in
free energy simulations using nonlinear mixing and a new functional form for so-called …

Advances in biomolecular simulation methods and access to large scale computer
resources have led to a massive increase in the amount of data generated. The key …

Background The structure and dynamics of DNA are critically related to its function.
Molecular dynamics simulations augment experiment by providing detailed information …