Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …

CHARMM‐GUI Membrane Builder, http://www. charmm‐gui. org/input/membrane, is a web‐
based user interface designed to interactively build all‐atom protein/membrane or …

As molecular dynamics (MD) simulations continue to evolve into powerful computational
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …

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

For molecular dynamics simulations of biological membrane systems to live up to the
potential of providing accurate atomic level detail into membrane properties and functions, it …

LOOS (Lightweight Object Oriented Structure‐analysis) is a C++ library designed to facilitate
making novel tools for analyzing molecular dynamics simulations by abstracting out the …

An increasing number of crystal structures available on one side, and the boost of
computational power available for computer-aided drug design tasks on the other, have …

Many novel broadly neutralizing antibodies against human immunodeficiency virus (HIV)
have been identified during the past decade, providing promising templates for the …

Here, a methodology is proposed to investigate the collective fluctuation modes of an
arbitrary set of observables, maximally contributing to the fluctuation of another functionally …

Objective The purpose of this work is to optimize the processing of molecular dynamics (MD)
trajectory data obtained for large biomolecular systems. Two popular software tools were …