Journal of molecular graphics最新文献

DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory under the auspices of the Council for the Central Laboratory of the Research Councils. Written to support academic research, it has a wide range of applications and is designed to run on a wide range of computers: from single processor workstations to parallel supercomputers. Its structure, functionality, performance, and availability are described.

This article describes a gradient algorithm for the computational optimization of model molecular structures, and discusses the various compromises inherent in the practical expression of the algorithm in a Fortran computer program (VULCAN) for both sequential and parallel computers. Details are given of some previously undiscussed properties of gradient algorithms; various acceleration techniques are compared: and some traps for the unwary are highlighted.

A three-dimensional (3-D) model of both subunits of interleukin 12 (IL-12) has been created through molecular modeling. Initial assignment of coordinates in the model of the p40 subunit was based on established amino acid sequence homology between the second and third domains of p40 and the human growth hormone receptor (GHR) and new observations of similarity between the first domain of p40 and the N-terminal domain of CD4. Human growth hormone (GH) served as the reference protein for the p35 chain. Furthermore, thorough analysis of the amino acid sequence of IL-12 revealed two distinct regions of the p40 subunit that display homology with other proteins. The first region (in domain two) contains the sequence RGD, which is found in adhesion proteins (such as fibronectin), and the nearby sequence VTCG, which occurs in a diverse set of molecules, including thrombospondin, properdin, and circumsporozoite proteins of Plasmodium. The second region of homology spans the third domain of p40 and shows marked similarity with the gastrointestinal peptides, such as secretin and glucagon and their preprohormones. We conclude (1) that the regions of homology define functionally important segments of p40 that are fully exposed at the protein surface, and (2) that the third domain of p40 (and its equivalent in the cytokine receptor family) is derived from the same ancestral genes as the gastrointestinal peptides.

Molecular dynamics simulations of biological systems are notoriously difficult to analyze because of the complexity of the information that they contain. We describe a new method for analyzing trajectories from simulations in order to extract important features of the motion. The trajectory of each atom is partitioned into conformation wells, in each of which its motion is assumed to be predominantly harmonic oscillation around an average position. Thus each atom moves anharmonically through a sequence of wells during the trajectory. The movement of atoms between wells, their ellipsoids of motion within each well, and correlations in the motion of atoms are quantified and can be visualized with molecular graphics. The TRAJAN analysis procedure is applicable to trajectories from equilibrium and nonequilibrium simulations and is not restricted to molecular dynamics simulations. Its application is demonstrated for a range of model systems.

We present potential maps of xenon in 20 different zeolites and molecular sieves. The potential maps reveal both the accessible pore volume and localized adsorption sites and so are important in understanding adsorption and diffusion processes in nanoporous materials. We examine zeolites and molecular sieves with one-dimensional channel-like nanopores (zeolite-Theta 1, AlPO₄-5, zeolite-Omega, zeolite-L, ZSM-12, AlPO₄-8, and VPI-5), with two-dimensional intersecting channel-like nanopores (ZSM-5 [silicalite], ZSM-11, ferrierite, mordenite, and zeolite-Beta), and with three-dimensionally connected cagelike nanopores (zeolite-A, zeolite-Rho, zeolite-Y, sodalite, chabazite, cloverite, cation-poor zeolite-A, and cation-rich zeolite-A). We report the fraction of pore volume accessible, the maximum energy well depth at the adsorption sites, and the activation energy to move between sites. We note several examples of surprising similarities and differences between various molecular sieves. In several instances, we show that these potential profiles are relevant for other small Lennard-Jones-like molecules. By comparison with published Monte Carlo and molecular dynamics simulations, we show that the density distributions of adsorbates at low density are well predicted by the potential maps.

In this article an analysis is performed of the results of stereogram construction using computer programs that model chemical compounds. Considerations about how best to represent models of molecules and improve legibility of stereograms are presented. An original diagrammatic substitute for the picture of a sphere, suitable for application in stereoscopic models of molecules, is proposed.