新型抗流感病毒药物——三羟基甲氧基黄酮分子对接的研究

运用柔性分子对接程序Affinity,深入研究了5,7,4'-三羟基-8-甲氧基黄酮(MF)与N1、N9亚型神经氨酸酶之间的结合方式并阐明其作用机制.结果表明MF与N1亚型神经氨酸酶之间有一种作用模式,其结合能为-70.26 kcal·mol-1,而与N9亚型之间存两种竞争性的结合模式,最大结合能为-83.51 kcal·mol-1.进一步分析发现MF与这两种亚型神经氨酸酶相互作用的作用力类型、氢键作用及关键作用的氨基酸残基等有着明显的区别.现行药物奥斯米韦作用模式单一,MF则可以与各种亚型甚至变异的神经氨酸酶发生很好地相互作用.因此,MF是一种极具应用前景的新型抗流感病毒药物.结合前人的研究成果,本研究提出了以MF为底物的流感药物修饰方向.     

The comparative molecular surface analysis (COMSA): a novel tool for molecular design

A new method allowing for 3-D QSAR analysis and the prediction of biological activity is presented. Unlike comparative molecular field analysis (CoMFA)-like techniques, it is based not on a comparison of the properties characterizing a discrete set of points but on the mean electrostatic potential (MEP) calculated and labeling specific areas defined on the molecular surface. A Kohonen self-organizing neural network and partial least square (PLS) analysis have been used for performing such an operation. The series of steroids complexing the corticosteroid (CBG) and testosterone (TBG) globulins, which forms a benchmark measuring the performance of the methods in molecular design, and a series of benzoic acids described by the Hammett sigma constants is used for testing the method. It is demonstrated that a method can be used efficiently to evaluate the responses determined both by the combination of electrostatic and steric effects or by electrostatic effects alone, therefore, two different schemes were developed. The first one, which involves PLS analysis of the full comparative networks, covers both steric and electrostatic effects. This scheme works well for both the CBG and TBG data. The second scheme takes into account only the properties (MEP) of these regions within molecules that can be superimposed with the template molecule. This scheme provides the best predictive power for the benzoic acids series. Comparison of the results from a CoMFA analysis proves that method is at least as effective for the responses limited by electrostatic effects, although it significantly outperforms CoMFA for CBG affinity which is dominated by steric effects.     

MolSpace: a computer desktop tool for visualization of massive molecular data

The authors have developed a software tool, MolSpace, to visualize massive molecular datasets. MolSpace can project a set of massive multivariate data onto a visual space (two- or three-dimensional space) by means of principal component analysis. MolSpace allows users not only to draw a scatter diagram of the data but also to display their two- or three-dimensional molecular structures as the objects in that space. With a probe (a molecular object) the user can navigate vast data spaces, thus facilitating understanding of the data structure. In addition, partial space searching is also available that is based on similarity searching techniques. It is possible to interrogate a three-dimensional structure of a chemical compound that corresponds to each object on the space in real time. The detail of the system is discussed with an illustrative example.     

LANDISVIEW: A visualization tool for landscape modelling

A major challenge in landscape and environmental modelling is to effectively visualize large amounts of time-series simulation output, often in various Geographic Information System (GIS) formats. We developed a software tool (LANDISVIEW), to easily visualize and animate time-series of ERDAS *.gis maps. The open source tool can also be used to generate batch files for FRAGSTATS, a widely used spatial analysis program.     

CTViz: A tool for the visualization of transport in nanocomposites

A visualization tool (CTViz) for charge transport processes in 3-D hybrid materials (nanocomposites) was developed, inspired by the need for a graphical application to assist in code debugging and data presentation of an existing in-house code. As the simulation code grew, troubleshooting problems grew increasingly difficult without an effective way to visualize 3-D samples and charge transport in those samples. CTViz is able to produce publication and presentation quality visuals of the simulation box, as well as static and animated visuals of the paths of individual carriers through the sample. CTViz was designed to provide a high degree of flexibility in the visualization of the data. A feature that characterizes this tool is the use of shade and transparency levels to highlight important details in the morphology or in the transport paths by hiding or dimming elements of little relevance to the current view. This is fundamental for the visualization of 3-D systems with complex structures. The code presented here provides these required capabilities, but has gone beyond the original design and could be used as is or easily adapted for the visualization of other particulate transport where transport occurs on discrete paths.     

A language for molecular visualization

The features and implementation of Pdbq, a special-purpose, interpreted language based on the C programing language, are described. Pdbq provides data types, control structures, operators, and built-in functions for specifying visualization mappings. The language arose from research into the specification of novel geometries from molecular data. Pdbq's data types, flow control, built-in functions, and global variables are discussed. Visualization examples using the language are presented     

A cache visualization tool

Improved cache performance is crucial to improved code performance. By visualizing cache behavior as the program is simulated, this memory analysis tool dynamically represents cache phenomena. The results can guide developers in making better software and hardware optimizations. The authors have developed a cache visualization tool which both dynamically visualizes cache content and provides related statistics     

ActiveGraph: A digital library visualization tool

ActiveGraph is an information visualization tool designed to provide users with a concise, customizable view of objects in a digital library. A set of digital library objects is represented as a data set in a two- or three-dimensional scatter plot. The data set can represent any digital library objects in any medium: books, journals, papers, images, Web resources, or even entire databases. Since ActiveGraph is intended for use in the context of digital libraries, data attributes consist for the most part of metadata fields such as title, author, date of publication, and number of citations. Data attributes are mapped to six visual attributes of the scatter plot: the X-, Y-, and Z-axes, color, size, and shape. The metadata for a selected data point are displayed in a control panel on the right-hand side of the screen. Users can edit the metadata and even add new metadata fields. Thus ActiveGraph allows users to both view and customize the contents of a library. Because of its flexibility in handling digital library objects and metadata of different types, ActiveGraph can be used in a variety of digital library applications. In this paper, we describe two: LibGraph, which is a visualization of a collaborative library, and CiteGraph, which is a visualization of citation statistics. Both applications were designed for use by scientists and engineers, for whom scatter plots are familiar and intuitive visualizations.     

A visualization tool for Y2K

To facilitate Y2K conversions, Bell Laboratories has developed a Y2K visualization tool. The input to the tool is the output of commercially available Cobol parsing tools that identify lines potentially affected by Y2K. While these tools are extremely useful, their output is daunting. Presenting this output visually increases assessment productivity by as much as 80 percent. Visualization also improves conversion quality by suggesting more-informed and efficient repair strategies. This visualization tool is based on the idea that no one view is sufficient to answer important questions concerning Y2K. It therefore provides a suite of tightly coupled, linked views. Each view is engineered for a particular task, is interactive, and is used for both display and analysis. Linking between views causes interactive operations to propagate instantly in each view. The authors report that the results to date have been promising. In one case, the time required for assessment and conversion strategy development dropped from three weeks to three days     

GrOWL: A tool for visualization and editing of OWL ontologies

In an effort to optimize visualization and editing of OWL ontologies we have developed GrOWL—a browser and visual editor for OWL that accurately visualizes the underlying DL semantics of OWL ontologies while avoiding the difficulties of the verbose OWL syntax. In this paper, we discuss GrOWL visualization model and the essential visualization techniques implemented in GrOWL.     

CASMI—A visualization tool for the World Stress Map database

The World Stress Map (WSM) project has compiled a global database of quality-ranked data records on the contemporary tectonic stresses in the Earth's crust. The WSM 2005 database release contains approximately 16 000 data records from different types of stress indicators such as earthquake focal mechanisms solutions, well bore breakouts, hydraulic fracturing and overcoring measurements, as well as quaternary fault-slip data and volcanic alignments. To provide a software tool for database visualization, analysis and interpretation of stress data as well its integration with other data records, we developed the program CASMI. This public domain software tool for Unix-like operating systems enables the selection of stress data records from the WSM database according to location, data quality, type of stress indicator, and depth. Each selected data record is visualized by a symbol that represents the type of stress indicator and the orientation of the maximum horizontal compressive stress. Symbol size is proportional to the quality of the data record, and the colour indicates different tectonic regimes. Stress maps can be produced in different geographical projections and high-quality output formats. CASMI also allows the integration of user-defined stress data sets and a wide range of other data such as topography, Harvard centroid moment tensors, polygons, text data, and plate motion trajectories. CASMI, including the WSM 2005 database release, can be requested free of charge from the project's website at http://www.world-stress-map.org/casmi. We present two stress map examples generated with CASMI ranging from plate-wide to regional scale: (1) A stress map of central Europe, that reveals the correlation of stress field orientation and relative plate motion. (2) The fan-shape stress pattern in North Germany.     

A novel machine vision application for analysis and visualization of confocal microscopic images

In this paper, a novel machine vision application is presented for analyzing and visualizing confocal microscopy images of biological preparations. The proposed system is divided into three subsystems: a 3D curved surface extraction subsystem that generates 3D surfaces passing through selected key points in confocal image stacks; a 2D image projection subsystem that produces a flattened projection of the extracted curved surface; and an image mosaic subsystem that concatenates a series of image projections to form a view of an entire biological preparation. A combination of cubic interpolation and boundary matching is employed to reconstruct the 3D curved surface that passes through selected key points. The projection process integrates data fidelity and local smoothness constraints, producing a color or intensity projection along the desired 3D surface. Registration is achieved by aligning and minimizing the sum of the squared distances (SSD) between the intensities of the corresponding pixels. Two biological applications of the proposed system are reported to illustrate how the vision system could aid in biological research.Received: 18 August 2003, Accepted: 18 March 2004, Published online: 4 November 2004 Correspondence to: David M. Chelberg     

VCMM: A visual tool for continuum molecular modeling

This paper describes the design and function of a visualization tool, VCMM, for visualizing and analyzing data, and interfacing solvers for generic continuum molecular modeling. In particular, an emphasis of the program is to treat the data set based on unstructured mesh as used in finite/boundary element simulations, which largely enhances the capabilities of current visualization tools in this area that only support structured mesh. VCMM is segmented into molecular, meshing and numerical modules. The capabilities of molecular module include molecular visualization and force field assignment. Meshing module contains mesh generation, analysis and visualization tools. Numerical module currently provides a few finite/boundary element solvers of continuum molecular modeling, and contains several common visualization tools for the numerical result such as line and plane interpolations, surface probing, volume rendering and stream rendering. Three modules can exchange data with each other and carry out a complete process of modeling. Interfaces are also designed in order to facilitate usage of other mesh generation tools and numerical solvers. We develop a technique to accelerate data retrieval and have combined many graphical techniques in visualization. VCMM is highly extensible, and users can obtain more powerful functions by introducing relevant plug-ins. VCMM can also be useful in other fields such as computational quantum chemistry, image processing, and material science.     

Traceview: a trace visualization tool

The design, development, and application of Traceview, a general-purpose trace-visualization tool that implements the trace-management and I/O features usually found in special-purpose trace-analysis systems, are described. The aspects of trace visualization that can be incorporated into a reusable tool are identified. The tradeoff in general-purpose design versus semantically based, detailed trace-data analysis is evaluated. Display methods and Traceview applications are discussed     

A cloud-enabled remote visualization tool for time-varying climate data analytics

The ever-growing time-varying climate datasets pose challenges for efficient analytics using the current desktop-based or generic remote visualization tools. We present a tightly-coupled scalable cloud-enabled remote visualization tool that exploits the computational capabilities of Graphical Processing Units (GPUs). We implement three typical volumetric/3D visualization techniques to illustrate the enhanced performance offered by remote GPU clusters. Our development also enables fast deployment to facilitate the access of remote analytics tools by a wide range of end users.     

A novel visualization model for web search results

This paper presents an interactive visualization system, named WebSearchViz, for visualizing the Web search results and acilitating users' navigation and exploration. The metaphor in our model is the solar system with its planets and asteroids revolving around the sun. Location, color, movement, and spatial distance of objects in the visual space are used to represent the semantic relationships between a query and relevant Web pages. Especially, the movement of objects and their speeds add a new dimension to the visual space, illustrating the degree of relevance among a query and Web search results in the context of users' subjects of interest. By interacting with the visual space, users are able to observe the semantic relevance between a query and a resulting Web page with respect to their subjects of interest, context information, or concern. Users' subjects of interest can be dynamically changed, redefined, added, or deleted from the visual space.     

Ptuba: a tool for the visualization of helix surfaces in proteins

Projection of transmembrane helices using a Uniform B-spline Algorithm is a tool for the visualization of interactions between helices in membrane proteins. It allows the user to generate projections of 3D helices, no matter what their deviations from a canonical helix might be. When associated with adapted coloring schemes it facilitates the comprehension of helix-helix interactions. Examples of transmembrane proteins were chosen to illustrate the advantages that this method provides. In the glycophorin A dimer we can easily appreciate the structural features behind homodimerisation. Using the structure of the fumarate reductase we analyze the contact surfaces inside a helical bundle and thanks to structures from a molecular dynamics simulation we see how modifications in structure and electrostatics relate to their interaction. We propose the use of this tool as an aid to the visualization and analysis of transmembrane helix surfaces and properties.     

A novel forensic image analysis tool for discovering double JPEG compression clues

This paper presents a novel technique to discover double JPEG compression traces. Existing detectors only operate in a scenario that the image under investigation is explicitly available in JPEG format. Consequently, if quantization information of JPEG files is unknown, their performance dramatically degrades. Our method addresses both forensic scenarios which results in a fresh perceptual detection pipeline. We suggest a dimensionality reduction algorithm to visualize behaviors of a big database including various single and double compressed images. Based on intuitions of visualization, three bottom-up, top-down and combined top-down/bottom-up learning strategies are proposed. Our tool discriminates single compressed images from double counterparts, estimates the first quantization in double compression, and localizes tampered regions in a forgery examination. Extensive experiments on three databases demonstrate results are robust among different quality levels. F ₁-measure improvement to the best state-of-the-art approach reaches up to 26.32 %. An implementation of algorithms is available upon request to fellows.     

基于演化设计的遗传算法在分子对接中的应用

将自然界的物种动态模型引入到遗传算法当中,反映出物种的真实进化状态,开发了基于演化设计的遗传算法。算法采用自适应策略克服了确定交叉和变异概率值的问题,利用小种群策略和最优保留策略保证了种群的多样性,改善了算法的寻优能力,进而提高了计算效率。运用该遗传算法求解分子对接优化模型,给出基于演化设计的分子对接程序。对接实例表明,算法能有效应用于分子对接问题中。     

PVaniM: a tool for visualization in network computing environments

Network computing has evolved into a popular and effective mode of high performance computing. Network computing environments have fundamental differences from hardware multiprocessors, involving a different approach to measuring and characterizing performance, monitoring an application's progress and understanding program behavior. In this paper, we present the design and implementation of PVaniM, an experimental visualization environment we have developed for the PVM network computing system. PVaniM supports a two-phase approach whereby on-line visualization focuses on large-grained events that are influenced by and relate to the dynamic network computing environment, and postmortem visualization provides for detailed program analysis and tuning. PVaniM's capabilities are illustrated via its use on several applications and a comparison with single-phase visualization environments developed for network computing. Our experiences indicate that, for several classes of applications, the two-phase visualization scheme can provide valuable insight into the behavior, efficiency and operation of distributed and parallel programs in network computing environments. © 1998 John Wiley & Sons, Ltd.