Lauren Wickstrom

TL;DR: Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution.

TL;DR: This work performs extensive replica-exchange molecular-dynamics simulations on Ala(3) and Ala(5) in TIP3P and TIP4P-Ew solvent models and suggests that the performance of ff99SB is among the best of currently available models.

TL;DR: An REMD variant in which the simulations are performed with a fully explicit solvent, but the calculation of exchange probability is carried out using a hybrid model, with the solvation shells calculated on the fly during the fully solvated simulation providing a dramatic decrease in the computational cost of REMD.

TL;DR: It is shown that even when perfect radii are used the agreement of GB with TIP3P DeltaDeltaG(pol) values does not improve, suggesting a limit to the optimization of the effective Born radius calculation and that future efforts to improve the accuracy of GB models must extend beyond such optimizations.

TL;DR: Interestingly, it is found that binding free energies are superior rank order predictors for a large subset containing the most flexible guests, which indicates that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies.