An understanding of molecular interactions is essential for insight into biological systems at
the molecular scale. Among the various components of molecular interactions, electrostatics …

The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …

A computational tool that offers accurate p K a values and atomically detailed knowledge of
protonation-coupled conformational dynamics is valuable for elucidating mechanisms of …

The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus
NonPolar (AGBNP) model we have previously reported, is presented with the aim of …

AcrB is the inner-membrane transporter of an E. coli AcrAB-TolC tripartite efflux complex,
which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB …

Infection with Lassa virus (LASV), an Old-World arenavirus that is endemic to West Africa,
causes Lassa fever, a lethal hemorrhagic fever. Delivery of LASV's genetic material into the …

Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their
structured targets. To obtain insight into the mechanism of formation of the electrostatic …

The ability of molecular dynamics simulation to capturing the transient states within the
folding pathway of protein is important to the understanding of protein folding mechanism. In …

Inspired by the idea of charge decomposition in calculation of the dipole preserving and
polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have …

Force field accuracy is still one of the “stalemates” in biomolecular modeling. Model systems
with high quality experimental data are valuable instruments for the validation and …