Shuanghong Huo

TL;DR: A historical perspective on the application of molecular dynamics to biological macromolecules is presented and recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed for the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories.

TL;DR: It is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results and the MM‐PBSA approach can be extended to rapid screening of a variety of possible modifications to binding sites.

TL;DR: Comparing the calculated and experimental binding free energies for a combinatorial library of inhibitors of cathepsin D (CatD), an aspartyl protease, offers hope that current methods of estimating the free energy of binding are accurate enough to be used in a multistep virtual screening protocol.

TL;DR: In this article, an algorithm for the calculation of reaction paths between known reactant and product states in systems of low or high dimension is described, defined as the path of maximum flux for a diffusive dynamics assuming isotropic friction.

TL;DR: In this paper, a solvation model based on weighted solvent accessible surface area (WSAS) is proposed to predict solvation free energies for both organic and biological molecules. But this model is not suitable for the solvation-free energy prediction problem.