Journal of molecular graphics最新文献

We outline a method for the calculation of multipole moments and molecular dipole-dipole (

Smectites, members¹ of the 2:1 layer silicate family, share the common feature that two tetrahedral sheets sandwich a sheet of octahedrally coordinated metal ion. The diversity of the members of the 2:1 layer silicates occurs because of their capacity for isomorphous substitution of various cations in the octahedral or tetrahedral sheets. Substitution of a divalent metal ion (such as Mg²⁺) for the trivalent Al³⁺ or a trivalent metal ion (such as Al³⁺) for the tetravalent silicon results in a net negative charge, which then undergoes interaction with positive ions (the exchangeable cations) to form an interlayer hydrated phase. Local density functional (LDF) calculations were employed to model isomorphous substitution of Al³⁺ by Na⁺, K⁺, Mg²⁺, Fe²⁺, and Fe³⁺ in the octahedral layer of a dioctahedral smectite clay such as montmorillonite. The energies of the isomorphous substitution were then compared with the experimental observation. The ordering for successful substitution is Al³⁺ > Fe³⁺ > Mg²⁺ > Fe²⁺ > Na⁺ < K⁺. This ordering is consistent with experimental observation. The vibrational frequencies for the isomorphous substituted systems were calculated by LDF calculation and were compared with the experimental IR results. The results match very well with experiment. This understanding will help in successful prediction of the catalytic activity of smectite clays.

Discriminant analysis applied to SAR studies using topological descriptors allows us to plot frequency distribution diagrams: a function of the number of drugs within an interval of values of discriminant function vs. these values. We make use of these representations, pharmacological distribution diagrams (PDDs), in structurally heterogeneous groups where generally they adopt skewed Gaussian shapes or present several maxima. The maxima afford intervals of discrimianant function in which exists a good expectancy to find new active drugs. A set of β-blockers with contrasted activity has been selected to test the ability of PDDs as a visualizing technique, for the identification of new β-blocker active compounds.

In this article we describe how the World Wide Web (WWW or Web) has been employed to provide access to computational chemistry software and protein structure data via program macros. We show how the combination of Web technology and macros can automate both the running of chemistry software and the execution of complex operations on protein structures. The current version of the system supports the molecular visualization packages GRASP,¹ RASMOL,² MOLVIEWER-OGL³ and INSIGHT95,⁴ and the ligand design tool GRID⁵ and includes more than 175 in-house protein-ligand complexes. The approach enables in-experienced users to confidently make full use of sophisticated modeling techniques by offering only sensible options, hiding parameter settings, and controlling program invocation and macro excution. Our interface provides both the expert and non-expert alike with powerful tools for protein structure visualization, molecular modeling, and rational drug design.

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiF_x)_n adsorbates on the Si{100} — (2 × 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterization of the SW potential. Theoretical and experimental work has demonstrated that the reactive fluorosilyl layer during siliconfluorine etching is composed of tower-like adspecies of SiF, SiF₂, and SiF₃ groups. The objective of the simulations is to determine how the chemical composition, mechanism of formation, and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate, the incident kinetic energy, and the parameterization of the potential energy function. Three reactions are simulated: F(g) + SiF₃(a), F(g) + SiF₂SiF₃(a), and F(g) + SiF₂SiF₂SiF₃(a). SiF₄ is the major product and Si₂F₆ and Si₃F₈ are minor products. In Si₂F₆ and Si₃F₈, the silicon-fluorine bond that is formed is stronger than the silicon-silicon bond in the molecule and, therefore, the majority of these products have enough energy to dissociate and will fragment before reaching the detector. An S_N2-like mechanism is the primary mechanism responsible for the formation of SiF₄, Si₂F₆, and Si₃F₈. In addition, at higher energies, the simulations have discovered a previously unknown mechanism for the formation of SiF₄, which involves an insertion between a silicon-silicon bond. The results of the simulations with the two potentials differ quite substantially in their prediction of the reactivity of the adsorbates. The SW potential predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section, especially for the SiF₄ product. These results are explained in terms of the differences in the potential energy functions used to describe the silicon-fluorine interactions. In addition, the results are compared to experimental data on silicon-fluorine etching.

STATIS, a data analysis method used when data can be expressed as matrices, seems particularly well suited to characterize the internal molecular motions and conformational states extracted from MD trajectories. We first outline this method and the “adapted STATIS” method. Applications are presented for 18-crown-6 (simulated for 2 nsec in acetonitrile solution) and for the (L30)₂Cu⁺ catenate (stimulated for 150 psec in chloroform). STATIS should be valuable for the classification of molecular conformations and simplified visualization of MD trajectories.

A three-dimensional model of human cathepsin E, a possible endothelin-converting enzyme, is constructed using computer-aided molecular modeling techniques. The structure of porcine pepsin, another aspartic protease, was used as a template. The final structure, after all gaps and deletions were made, was optimized using the AMBER-4 package. A dipeptide (Trp-Val) representing the substrate was docked in the putative active site and the whole structure was optimized after several runs of minimization and dynamics calculations. The result of this modeling study showed that the structure of cathepsin E is similar to that of porcine pepsin and has three disulfide bonds that are conserved in both enzymes. There are two Asp-Thr-Gly sequences at the active site of enzyme. The active site cavity is large enough to accommodate its substrate.

STRUCTURELAB is a computational system that has been developed to permit the use of a broad array of approaches for the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences. The approach taken views the structure determination problem as one of dealing with a database of many computationally generated structures and provides the capability to analyze this data set from different perspectives. Many algorithms are integrated into one system that also utilizes a heterogeneous computing approach permitting the use of several computer architectures to help solve the posed problems. These different computational platforms make it relatively easy to incorporate currently existing programs as well as newly developed algorithms and to best match these algorithms to the appropriate hardware. The system has been written in Common Lisp running on SUN or SGI Unix workstations, and it utilizes a network of participating machines defined in reconfigurable tables. A window-based interface makes this heterogeneous environment as transparent to the user as possible.