GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: A formula is derived for the underlying cause of artifacts in the case of the Langevin thermostat, and it is found it vanishes slowly as the inverse square root of the number of time steps per simulation segment.

TL;DR: Molecular modeling of the SsNAC23 3-D structure and its nuclear localization suggest that this protein has conserved transcription factor domains, indicating that this gene is involved in the response to extreme low temperature stress.

TL;DR: It is found that inclusion of the electron gas in the model slows down the Coulomb explosion, and suggests that by using ultrashort exposures, structural information may be collected before the sample is destroyed due to radiation damage.

TL;DR: This model concluded that the initial high-affinity drug-binding site was located in the interfacial surface area of P-glycoprotein in contact with the membrane interface, which suggests that most transported drugs are concentrated near the surface zone of the inner leaflet of the plasma membrane.

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.