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.     

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     

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     

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 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.     

A visualization tool of 3-D time-varying data for the simulation of tissue growth

Data Visualization affords us the ability to explore the spatial and temporal domains of many time-varying phenomena. In this article, we describe our application of visualization to a three-dimensional simulation model for tissue growth. We review the different components of the model where cellular automata is used to model populations of cells that execute persistent random walks, collide, and proliferate until they reach confluence. We then describe the system architecture of the developed visualization tool, the employed rendering techniques, and the related prototyping interfaces. We also discuss some of the visualization results obtained thus far that are pertinent to enhancing the validity of the computational model. This visualization tool could be useful in facilitating the research of scientists by providing them with meaningful means to interpret and analyze simulation data and to compare them to experimental results. Our objective in this work is to develop computer-aided design solutions that support the simulation of tissue growth and its design exploration.     

A novel three-tiered visualization approach for firewall rule validation

Firewall is one of the most critical elements of the current Internet, which can protect the entire network against attacks and threats. While configuring the firewalls, rule configuration has to conform to, or say be consistent with, the demands of the network security policies such that the network security would not be flawed. For the security consistency, firewall rule editing, ordering, and distribution must be done very carefully on each of the cooperative firewalls, especially in a large-scale and multifirewall-equipped network. Nevertheless, a network operator is prone to incorrectly configure the firewalls because there are typically thousands or hundreds of filtering/admission rules (i.e., rules in the Access Control List file, or ACL for short), which could be set up in a firewall; not mentioning these rules among firewalls affect mutually and can make the matter worse. Under this situation, the network operator would hardly know his/her misconfiguration until the network functions beyond the expectation. For this reason, our work is to build a visualized validation system for facilitating the check of security consistency between the rule configuration of firewalls and the demands of network security policies. To do so, the developed validation system utilizes a three-tiered visualization hierarchy along with different compound viewpoints to provide users with a complete picture of firewalls and relationships among them for error debugging and anomaly removal. In addition, in this paper, we also enumerate the source of security inconsistency while setting ACLs and make use of it as a basis of the design of our visualization model. Currently, part of the firewall configuration of our campus network has been used as our system's input to demonstrate our system's implementation.     

Multimedia tool suite for the visualization of drama heritage metadata

This paper presents a multimedia tool suite for, on the one hand, the annotation of metadata that encode the dramatic qualities of cultural heritage items, and, on the other, the visualization of such metadata for drama analysis and didactics. The tool suite relies upon an ontology of drama to devise an annotation schema for the metadata concerning the dramatic qualities. The two major modules of the tool suite are a web-based platform, that allows for the insertion of the annotation metadata, and a visualization program for the interactive exploration of such metadata, respectively. The tool suite was tested on the cross-media studies of drama analysis and teaching of drama structure through the application to classical examples.     

A novel tool for summarization of arthroscopic videos

Arthroscopic surgery is a minimally invasive procedure that uses a small camera to generate video streams, which are recorded and subsequently archived. In this paper we present a video summarization tool and demonstrate how it can be successfully used in the domain of arthroscopic videos. The proposed tool generates a keyframe-based summary, which clusters visually similar frames based on user-selected visual features and appropriate dissimilarity metrics. We discuss how this tool can be used for arthroscopic videos, taking advantage of several domain-specific aspects, without losing its ability to work on general-purpose videos. Experimental results confirm the feasibility of the proposed approach and encourage extending it to other application domains.     

MOLVIE: an interactive visualization environment for molecular structures

A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.     

VU-flow: a visualization tool for analyzing navigation in virtual environments

This paper presents a tool for the visual analysis of navigation patterns of moving entities, such as users, virtual characters or vehicles in 3D virtual environments (VEs). The tool, called VU-Flow, provides a set of interactive visualizations that highlight interesting navigation behaviors of single or groups of moving entities that were the VE together or separately. The visualizations help to improve the design of VEs and to study the navigation behavior of users, e.g., during controlled experiments. Besides VEs, the proposed techniques could also be applied to visualize real-world data recorded by positioning systems, allowing one to employ VU-Flow in domains such as urban planning, transportation, and emergency response     

量子粒子群优化智能算法的高精度分子对接方法研究

分子对接是药物发现与设计的重要方法,采用计算机优化和模式识别方法在三维结构数据库中搜索几何、化学特性与特定药物结合位点相匹配分子的计算机辅助药物筛选是当前分子对接的研究热点,这种问题可以归为参数优化问题。本文提出了一种基于改进的量子粒子群(quantum-behaved particle swarm optimization,QPSO)算法的分子对接方法,用于处理大自由度的分子对接计算,并与基于标准QPSO算法和经典拉马克遗传算法的分子对接方法进行了比较,实验结果表明新方法无论是在对接能量还是对接准确性上,明显优于其它2种方法,尤其是在配体复杂性不断增加的情况下,非常适用于高柔性分子对接问题。