GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: The findings presented here are promising for future bio-imaging experiments with X-ray free electron lasers, and they strongly support the validity of mass spectrometry experiments for studies of intra- and intermolecular interactions.

TL;DR: It is demonstrated, through a total sum of 1.6 μs of biophysical simulations, that 09N1 NA exists in solution preferentially with an open 150-cavity, providing an atomic-level structural understanding of the recent finding that antiviral compounds designed to take advantage of contacts in the 150-Cavity can inactivate both 2009 H1N1 pandemic and avian H5N1 viruses.

TL;DR: The aggregation behavior of two bile acid salts has been studied in their aqueous solutions of three different concentrations by means of molecular dynamics computer simulations and has revealed that, due to their molecular structure, which is markedly different from that of the ordinary aliphatic surfactants, the bile ions form rather different aggregates than the usual spherical micelles.

TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.

Abstract: The structures of the three major classes of biopolymers-polynucleotides, polypeptides and polysaccharides-are surveyed in the light of the most recent results from X-ray diffraction, electron microscopy and other studies. The review contains an introductory section setting out the basic features of each class of biopolymer: the natures of the 'building blocks', the linkages between them, conformational principles, types of repeating (secondary) structures and so on. The main section on each class is deliberately selective, because of the large amount of structural information now available. The section on polynucleotides concentrates on DNA, reviewing the classical double-helical models and the evidence provided by X-ray fibre diffraction, but also paying special attention to the rapid growth of new information on such features as the variations in helix geometry and in base-stacking, those data being derived primarily from studies of small self-complementary oligonucleotides. Alternative models and the question of right-handed versus left-handed structures are also considered. Among polypeptide structures, both globular and fibrous proteins are described. Globular proteins are treated as a group, with no detailed description of any one of them; this section concentrates on the organisation of globular proteins via folding units and domains, some general features (protein homology, catalysis, flexibility, interaction with water), membrane proteins, immunoglobulins and viruses.

TL;DR: A comparison of a series of extended molecular dynamics simulations of bacteriophage T4 lysozyme in solvent with X‐ray data is presented, revealing that the N‐terminal helix rotates together with either of these two domains.