Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …

Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

Molecular dynamics simulations have evolved into a mature technique that can be used
effectively to understand macromolecular structure-to-function relationships. Present …

Recent advances in molecular simulations have allowed scientists to investigate slower
biological processes than ever before. Together with these advances came an explosion of …

All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …

The immunostimulatory cytokine interleukin-2 (IL-2) is a growth factor for a wide range of
leukocytes, including T cells and natural killer (NK) cells,,. Considerable effort has been …

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 …

MSMBuilder is a software package for building statistical models of high-dimensional time-
series data. It is designed with a particular focus on the analysis of atomistic simulations of …

Simulations can provide tremendous insight into the atomistic details of biological
mechanisms, but micro-to millisecond timescales are historically only accessible on …