We reassess progress in the field of biomolecular modeling and simulation, following up on
our perspective published in 2011. By reviewing metrics for the field's productivity and …

The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …

Recent advances in computational hardware and free energy algorithms enable a broader
application of molecular simulation of binding interactions between receptors and small …

Molecular mechanics (MM) simulations have the potential to provide detailed insights into
the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities …

We present E2EDNA, a simulation protocol and accompanying code for the molecular
biophysics and materials science communities. This protocol is both easy to use and …

Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in
modulating protein functions through binding and/or catalytically activating proteins …

Abstract Magnesium (Mg 2+), the second most abundant intracellular cation, plays a crucial
role in cellular functions. In this study, we investigate the interaction between Mg 2+ and …

The organization of genomes in space and time dimension plays an important role in gene
expression and regulation. Chromatin folding occurs in a dynamic, structured way that is …

Metal ions are ubiquitous in complex with proteins and play key roles in protein structure
and function. The ion-protein interactions are electrostatic delicate in nature, however, the …

Although β-actin is one of only two ubiquitously expressed actin isoforms present in all cells,
it remains understudied biochemically due to technical challenges associated with protein …