Huafeng Xu

TL;DR: Two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+.

TL;DR: A contemporary overview of the scientific, technical, and practical issues associated with running relative BFE simulations in AMBER20 is provided, with a focus on real-world drug discovery applications.

TL;DR: In this paper, the particle-particle particle-mesh (P3M) method is combined with the reversible reference system propagator algorithm (RESPA) for treating the multiple time scale problems in the molecular dynamics of complex systems with multiple time scales and long-range forces.

TL;DR: Long time scale fragment binding simulations of sufficient length are performed, allowing the binding affinities, on- and off-rates, and relative occupancies of alternative binding sites and alternative poses within each binding site to be estimated, thereby illustrating the potential of long time scale MD as a quantitative tool for fragment-based drug discovery.

TL;DR: The method can reveal the underlying geometry of the manifold without intensive nearest-neighbor or shortest-path computations and can reproduce the true geodesic distances of the data points in the low-dimensional embedding without requiring that these distances be estimated from the data sample.