An efficient and flexible scanning of databases of protein secondary structures

Protein secondary structure describe protein construction in terms of regular spatial shapes, including alpha-helices, beta-strands, and loops, which protein amino acid chain can adopt in some of its regions. This information is supportive for protein classification, functional annotation, and 3D structure prediction. The relevance of this information and the scope of its practical applications cause the requirement for its effective storage and processing. Relational databases, widely-used in commercial systems in recent years, are one of the serious alternatives honed by years of experience, enriched with developed technologies, equipped with the declarative SQL query language, and accepted by the large community of programmers. Unfortunately, relational database management systems are not designed for efficient storage and processing of biological data, such as protein secondary structures. In this paper, we present a new search method implemented in the search engine of the PSS-SQL language. The PSS-SQL allows formulation of queries against a relational database in order to find proteins having secondary structures similar to the structural pattern specified by a user. In the paper, we will show how the search process can be accelerated by multiple scanning of the Segment Index and parallel implementation of the alignment procedure using multiple threads working on multiple-core CPUs.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiring the use of computer programs offering high-resolution analysis and comparison of nucleotide sequence data. The strategy involves the development of a pair of computer programs, called SEQANAL and SEQTALK, designed to operate in tandem. SEQANAL is a large and complex program intended to be used to discover regions of internal repeats and dyad symmetries within one sequence, or regions of homology, complementarity or optimal alignment between two sequences. Three algorithms are supported: those of Staden (1977, 1978); of Korn et al. (1977); Queen and Korn (1980); and the newly-described exhaustive tree-searching algorithm of Burnett et al. (1985, 1986). The SEQTALK program is a small, portable, interactive, front-end program with which the user can specify the instructions to control the SEQANAL program. Together, the SEQANAL and SEQTALK programs permit analyses to be performed at a remote facility on a mainframe computer under the complete control of a distant user equipped with minimal computing facilities, and without needing networking facilities.     

Application of an analytical model to evaluate storage structures

The File Design Analyzer is a software package which evaluates well-known data base storage structures and access methods in terms of secondary storage processing time and storage overhead required to service a set of user applications. It implements a first-order analytical model to specifically evaluate sequential, indexed sequential, direct access, and inverted multilist storage structures. Interaction with the package is available in conversational mode, enabling the experienced analyst to conduct on-line sensitivity analysis.The paper describes three extensions which converted an abstract conceptual model into a practical tool for evaluation of existing or proposed data base designs: batched transactions, multi-access interference due to shared secondary storage, and analysis of variable record size. A case study from a real system illustrates the potential of the File Design Analyzer to provide insight regarding the optimal choice of physical parameters within a specified storage structure and to effectively compare alternative storage structures for a particular set of applications.     

Comparing multiple RNA secondary structures using tree comparisons.

In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.     

Visualizing protein conformational changes on a personal computer--alpha carbon pseudo bonding as a constraint for interpolation in internal coordinate space

A Java program has been developed to produce animations and movies of protein conformation changes. The animations, primarily intended for teaching purposes, are produced by visualizing a series of aligned structures interpolated between two forms of the same protein. To produce plausible intermediate structures, the interpolation is performed in internal coordinate space and uses a simple constraint to avoid the production of artifactual movements of the protein backbone. This constraint involves the introduction of 'pseudo' bonds linking the protein alpha carbon atoms. All of the steps from alignment of initial structures to the production of AVI movies can be performed on readily available personal computers.     

Single‐View Modeling of Layered Origami with Plausible Outer Shape

Modeling 3D origami pieces using conventional software is laborious due to the geometric constraints imposed by the complicated layered structure. Targeting origami models used in visual content such as CG illustrations and movies, we propose an interactive system that dramatically simplifies the modeling of 3D origami pieces with plausible outer shapes, while omitting accurate inner structures. By focusing on flat origami models with a front‐and‐back symmetry commonly found in traditional artworks, our system realizes easy and quick modeling via single‐view interface; given a reference image of the target origami piece, the user draws polygons of planar faces onto the image, and assigns annotations indicating the types of folding operations. Our system automatically rectifies the manually‐specified polygons, infers the folded structures that should yield the user‐specified polygons with reference to the depth order of layered polygons, and generates a plausible 3D model while accounting for gaps between layers. Our system is versatile enough for modeling pseudo‐origami models that are not realizable by folding a single sheet of paper. Our user study demonstrates that even novice users without the specialized knowledge and experience on origami and 3D modeling can create plausible origami models quickly.     

Computerized optimization of bridge structures

A unified bridge design optimization theory has been developed by a research team composed of personnel from the College of Engineering, Louisiana State University working in close collaboration with engineers from the Louisiana Department of Highways. The theory, useful in the design of multispan, simply supported highway bridges considers simultaneously the structure and the geometry of the bridge. Soil and terrain conditions, construction costs, shape, and other parameters can be investigated simultaneously with dynamic programming, an optimization technique applicable to serial systems of the type to which these structures belong.A computer program developed and now completely operational provides the bridge design engineer with an efficient, flexible tool for evaluating a multitude of preliminary designs. The average Central Processing Unit time required for a typical bridge is in the order of l min per spanonanIBM360/65configuration.The program generates the lowest cost bridge and all other bridge structures that fall within any specified percentage of the minimum cost (1 or 2 per cent, for example). The range is specified by the user. In addition the program has cycling capabilities for selecting the most economical configuration (number, lengths and types of spans).Costs, soil conditions, geometry, material properties, and types of decks, girders and bents are specified by the designer such that the program can be used as a simulation tool for selecting the most economical structure quickly and efficiently. Constraints can be imposed upon the bridge geometry by specifying locations of bents or span center lines or both, to account for special conditions such as bridge crossings, existing roadways, and other physical obstructions.The optimization program is modular and operates heuristically, that is, it permits full man-machine interaction not only through the input of data but also through structural design module interehangeability allowing the user to incorporate his own procedures as subroutines.The complete program is fully documented with a users manual and a programmers manual.     

Unsupervised manifold alignment using soft-assign technique

In this paper, we propose a robust unsupervised algorithm for automatic alignment of two manifolds in different datasets with possibly different dimensionalities. The significant contribution is that the proposed alignment algorithm is performed automatically without any assumptions on the correspondences between the two manifolds. For such purpose, we first automatically extract local feature histograms at each point of the manifolds and establish an initial similarity between the two datasets by matching their histogram-based features. Based on such similarity, an embedding space is estimated where the distance between the two manifolds is minimized while maximally retaining the original structure of the manifolds. The elegance of this idea is that such complicated problem is formulated as a generalized eigenvalue problem, which can be easily solved. The alignment process is achieved by iteratively increasing the sparsity of correspondence matrix until the two manifolds are correctly aligned and consequently one can reveal their joint structure. We demonstrate the effectiveness of our algorithm on different datasets by aligning protein structures, 3D face models and facial images of different subjects under pose and lighting variations. Finally, we also compare with a state-of-the-art algorithm and the results show the superiority of the proposed manifold alignment in terms of vision effect and numerical accuracy.     

Creation of a file translation language for networks

The rapid growth of large, national computer networks (as exemplified by ARPA) has created a serious problem in the sharing of information between incompatible systems. These incompatibilities can be either physical, contextual, or organizational in nature. A special-purpose, high-level language, entitled FTL, is proposed as a possible solution. With FTL a user initially views his information as an unbounded binary bit stream without artificial boundaries or predetermined meanings. The statements and primitives in FTL allow a user to first impose any structure desired on the input bit stream and secondly to restructure the information into a form that will allow it to be compatible with the conventions of the destination node. The subsequent execution of an FTL program will actually effect a translation of the specified input file into the desired output file.     

Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution

Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.     

Computer-aided optimum design of steel tubular telescopic pole structures

This paper presents a computer-aided approach for the optimum design of steel tubular telescopic pole structures. The author's experience in steel pole structure's design is implemented in a computer program called ODAPS (optimum design and analysis of pole structures). Although several other computer programs exist for the analysis and design of steel tubular pole structures, they are limited to cases where dimensions are pre-defined by the user. Different from these conventional programs, the developed program is able to automatically design the pole structure having the lightest weight that satisfies the limits states criteria within given geometrical boundary conditions. Simple equations and charts for the design of poles of different steel grade and having different length, subjected to various point loads at their top, are obtained using this program. It is possible to obtain economical designs for pole structures subjected to a specified loading using these equations or charts.     

Characterizing user performance in command-driven dialogue

To learn to use an interactive system, a person typically has to acquire a good deal of new knowledge. The ease of learning will depend on the extent to which the design of the task and the interface capitalizes on the user's pre-existing knowledge and his or her cognitive capabilities for learning. This paper explores the nature of both design decisions and user learning with a command-based system. Three studies were conducted, all involving a task in which secret messages were decoded by means of a sequence of commands (based on the task used by Barnard et al. In Study I, software specialists designed command structures for the task and gave reasons for their choices. In Study II, naive subjects chose between alternative command terms. In Study TTI, subjects learned to use interactive versions of the task in which dialogue factors (command terms and argument structures) were systematically varied. The results enabled the development of user knowledge of the system to be specified in detail. Comparisons across the three studies highlighted the diversity of the factors determining both design decisions and user behaviour.     

带2~(1/2)细分结构的四边形化

在Morse函数理论的基础上,提出一种新的从三角网格中建立四边形网格多分辨率表示的方法.先由人工指定或从拉普拉斯矩阵的特征函数中提取临界点,计算带约束的拉普拉斯方程得到光滑的Morse函数.函数的临界点(极大、极小和鞍点)有规律地分布在模型表面,在三角网格表面梯度场的引导下,生成临界点间流线,得到临界点间的拓扑关系.通过临界点交换规则,同样是采用流线的方法,得到更精细的四边形网格。最终可实现无需参数化而仅用流线方法来建立不同多分辨率表示的四边形网格。     

Tree pattern mining with tree automata constraints

Most work on pattern mining focuses on simple data structures such as itemsets and sequences of itemsets. However, a lot of recent applications dealing with complex data like chemical compounds, protein structures, XML and Web log databases and social networks, require much more sophisticated data structures such as trees and graphs. In these contexts, interesting patterns involve not only frequent object values (labels) appearing in the graphs (or trees) but also frequent specific topologies found in these structures. Recently, several techniques for tree and graph mining have been proposed in the literature. In this paper, we focus on constraint-based tree pattern mining. We propose to use tree automata as a mechanism to specify user constraints over tree patterns. We present the algorithm CoBMiner which allows user constraints specified by a tree automata to be incorporated in the mining process. An extensive set of experiments executed over synthetic and real data (XML documents and Web usage logs) allows us to conclude that incorporating constraints during the mining process is far more effective than filtering the interesting patterns after the mining process.     

A City Metaphor to Support Navigation in Complex Information Spaces

A major problem in modern information systems is to locate information and to re-find information one has seen before. Systems like the World Wide Web are heavily interlinked, but do not show structures that help users to navigate the information it contains. The use of appropriate navigation metaphors can help to make the structure of modern information systems easier to understand and therefore easier to use.We propose a conceptual user interface metaphor based on the structure of a city. Cities are very complex spatial environments and people know how to get information, how to reach certain locations in a city, and how to make use of the available infrastructure, etc. Cities provide a rich set of navigational infrastructure that lends itself to creating sub-metaphors for navigational tools. A city metaphor makes this existing knowledge about a structured environment available to the user of a computerized information system.We first focus on several properties necessary for future user interfaces (or user interface metaphors) that will distinguish them from current systems, like the richness of information or the use of visualizations to show the structure of information spaces. We also describe the strengths and problems of spatial user-interface metaphors. Then we present the structure of the information city metaphor, its structuring and navigation metaphors and what we see as its main advantages and problems. We further outline a few scenarios of how an Information City might work. Finally, we compare implementing this metaphor using either a textual or a graphical virtual environment or a combination.     

Mutation Mining—A Prospector's Tale

Protein structure visualization tools render images that allow the user to explore structural features of a protein. Context specific information relating to a particular protein or protein family is, however, not easily integrated and must be uploaded from databases or provided through manual curation of input files. Protein Engineers spend considerable time iteratively reviewing both literature and protein structure visualizations manually annotated with mutated residues. Meanwhile, text mining tools are increasingly used to extract specific units of raw text from scientific literature and have demonstrated the potential to support the activities of Protein Engineers. The transfer of mutation specific raw-text annotations to protein structures requires integrated data processing pipelines that can co-ordinate information retrieval, information extraction, protein sequence retrieval, sequence alignment and mutant residue mapping. We describe the Mutation Miner pipeline designed for this purpose and present case study evaluations of the key steps in the process. Starting with literature about mutations made to protein families; haloalkane dehalogenase, bi-phenyl dioxygenase, and xylanase we enumerate relevant documents available for text mining analysis, the available electronic formats, and the number of mutations made to a given protein family. We review the efficiency of NLP driven protein sequence retrieval from databases and report on the effectiveness of Mutation Miner in mapping annotations to protein structure visualizations. We highlight the feasibility and practicability of the approach. Funding project: Ontologies, the semantic web and intelligent systems for genomics Génome Québec, 630, boul. René-Lévesque Ouest, bureau 2660, Montréal (Québec) H3B 1S6, e-mail: gqinfo@genomequebec.com     

Immersive structural biology: a new approach to hybrid modeling of macromolecular assemblies

Advanced biophysical imaging techniques, such as cryo-electron microscopy or tomography, enable 3D volumetric reconstructions of large macromolecular complexes in a near-native environment. However, pure volumetric data is insufficient for a detailed understanding of the underlying protein–protein interactions. This obstacle can be overcome by assembling an atomic model of the whole protein complex from known atomic structures, which are available from either X-ray crystallography or homology modeling. Due to many factors such as noise, conformational variability, experimental artifacts, and inexact model structures, existing automatic docking procedures are known to report false positives for a significant number of cases. The present paper focuses on a new technique to combine an offline exhaustive search algorithm with interactive visualization, collision detection, and haptic rendering. The resulting software system is highly immersive and allows the user to efficiently solve even difficult multi-resolution docking problems. Stereoscopic viewing, combined with head tracking and force feedback, generates an ideal virtual environment for true interaction with and solution of hybrid biomolecular modeling problems.     

Minimizing user intervention in registering 2D images to 3D models

This paper proposes a novel technique to speed up the registration of 2D images to 3D models. This problem often arises in the process of digitalization of real objects, because pictures are often taken independently from the 3D geometry. Although there are a number of methods for solving the problem of registration automatically, they all need some further assumptions, so in the most general case the process still requires the user to provide some information about how the image corresponds to geometry, for example providing point-to-point correspondences. We propose a method based on a graph representation where the nodes represent the 2D photos and the 3D object, and arcs encode correspondences, which are either image–to–geometry or image–to–image point pairs. This graph is used to infer new correspondences from the ones specified by the user and from successful alignment of single images and to factually encode the state of the registration process. After each action performed by the user, our system explores the states space to find the shortest path from the current state to a state where all the images are aligned, i.e. a final state and, therefore, guides the user in the selection of further alignment actions for a faster completion of the job. Experiments on empirical data are reported to show the effectiveness of the system in reducing the user workload considerably.     

An automatic homology modeling method consisting of database searches and simulated annealing

We introduce a method of homology modeling consisting of database searches and simulated annealing. All processes involving searches for homologous proteins, alignment, the construction of Calpha atoms, construction of main-chain atoms, and the construction of side-chain atoms are performed automatically. In this method, main-chain conformations are generated from the weighted average of mainchain coordinates in reference proteins. The weight is defined by the local space homology representing the similarity of environmental residues at topologically equivalent positions in reference proteins. Side-chain conformations are generated for constructed main-chain atoms by database searches, and main-chain atoms are optimized for the fixed side-chain conformations. These two processes, i.e., the side-chain generation and main-chain optimization, are repeated several times. This type of construction provides a structure similar to the x-ray structure, in particular, for main-chain and side-chain atoms in the residues belonging to structurally conserved regions (SCRs). The accuracy of our method was evaluated for 14 proteins whose structures are known. The average root mean square deviation between models and x-ray structures was 2.29 A for all atoms, and the percentage of chi1 angles within 30 degrees was 72.6% for SCRs residues. Some models were in good agreement with their respective x-ray structures. Our method, which has the advantage of being automated, gives results similar to, or better than, published results for three widely used test proteins. Our software, FAMS, is available on the World Wide Web.