Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a
potentially useful tool for accelerating molecular dynamics (MD) simulations. By …

This Review illustrates the evaluation of permeability of lipid membranes from molecular
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …

Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …

The accuracy of atomistic biomolecular modeling and simulation studies depend on the
accuracy of the input structures. Preparing these structures for an atomistic modeling task …

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

CHARMM is an academic research program used widely for macromolecular mechanics
and dynamics with versatile analysis and manipulation tools of atomic coordinates and …