Simulating protein folding has been a challenging problem for decades due to the long
timescales involved (compared with what is possible to simulate) and the challenges of …

Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus
have the potential to provide near universal protection against influenza virus infection …

The application of quantum chemical, automatic multilevel modeling workflows for the
determination of thermodynamic (eg, conformation equilibria, partition coefficients, p K a …

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely
available computer programs for the analysis and processing of time series of three …

The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of
macromolecular structures and dynamics. As increasingly larger macromolecular systems …

We propose a fully-automated composite scheme for the accurate and numerically stable
calculation of molecular entropies by efficiently combining density-functional theory (DFT) …

The quantitative assessment of uncertainty and sampling quality is essential in molecular
simulation. Many systems of interest are highly complex, often at the edge of current …

Modern computational chemistry has reached a stage at which massive exploration into
chemical reaction space with unprecedented resolution with respect to the number of …