GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: A PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment is proposed and can be coupled with DSSP and thus opens a simple way for further analysis in this field.

TL;DR: In this paper, a new way to calculate the electrostatic properties of macromolecules was proposed, which goes beyond the classical Poisson-Boltzmann treatment with only a small extra CPU cost.

TL;DR: In this paper, the authors reflect on the current understanding on interfacing nanomaterials such as carbon nanotubes and fullerenes with biological systems and propose strategies for improving the solubility and therefore, the bioavailability of nanommaterials in aqueous solutions.

TL;DR: In this article , a rational electrolyte design is proposed to stabilize the interfaces between the electrolyte and both the lithium metal anode and the high voltage cathode in future rechargeable Li metal batteries.

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.