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Selected AbstractsDomain,ligand mapping for enzymesJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2010Matthew Bashton Abstract In this paper we provide an overview of our current knowledge of the mapping between small molecule ligands and protein domains. We give an overview of the present data resources available on the Web, which provide information about protein,ligand interactions, as well as discussing our own PROCOGNATE database. We present an update of ligand binding in large protein superfamilies and identify those ligands most frequently utilized by nature. Finally we discuss potential uses for this type of data. Copyright © 2009 John Wiley & Sons, Ltd. [source] Mining related queries from Web search engine query logs using an improved association rule mining modelJOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 12 2007Xiaodong Shi With the overwhelming volume of information, the task of finding relevant information on a given topic on the Web is becoming increasingly difficult. Web search engines hence become one of the most popular solutions available on the Web. However, it has never been easy for novice users to organize and represent their information needs using simple queries. Users have to keep modifying their input queries until they get expected results. Therefore, it is often desirable for search engines to give suggestions on related queries to users. Besides, by identifying those related queries, search engines can potentially perform optimizations on their systems, such as query expansion and file indexing. In this work we propose a method that suggests a list of related queries given an initial input query. The related queries are based in the query log of previously submitted queries by human users, which can be identified using an enhanced model of association rules. Users can utilize the suggested related queries to tune or redirect the search process. Our method not only discovers the related queries, but also ranks them according to the degree of their relatedness. Unlike many other rival techniques, it also performs reasonably well on less frequent input queries. [source] Highly Robust Estimation of the Autocovariance FunctionJOURNAL OF TIME SERIES ANALYSIS, Issue 6 2000Yanyuan Ma In this paper, the problem of the robustness of the sample autocovariance function is addressed. We propose a new autocovariance estimator, based on a highly robust estimator of scale. Its robustness properties are studied by means of the influence function, and a new concept of temporal breakdown point. As the theoretical variance of the estimator does not have a closed form, we perform a simulation study. Situations with various size of outliers are tested. They confirm the robustness properties of the new estimator. An S-Plus function for the highly robust autocovariance estimator is made available on the Web at http://www-math.mit.edu/~yanyuan/Genton/Time/time.html. At the end, we analyze a time series of monthly interest rates of an Austrian bank. [source] Soft protein,protein docking in internal coordinatesPROTEIN SCIENCE, Issue 2 2002Juan Fernández-Recio PDB, Protein Data Bank; ICM, Internal Coordinate Mechanics; RMSD, root-mean-square deviation Abstract The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased the speed of the procedure. The method was tested on a benchmark of 24 protein,protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations. The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web. [source] A large-scale monitoring and measurement campaign for web services-based applicationsCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 10 2010Riadh Ben Halima Abstract Web Services (WS) can be considered as the most influent enabling technology for the next generation of web applications. WS-based application providers will face challenging features related to nonfunctional properties in general and to performance and QoS in particular. Moreover, WS-based developers have to provide solutions to extend such applications with self-healing (SH) mechanisms as required for autonomic computing to face the complexity of interactions and to improve availability. Such solutions should be applicable when the components implementing SH mechanisms are deployed on both or only one platform on the WS providers and requesters sides depending on the deployment constraints. Associating application-specific performance requirements and monitoring-specific constraints will lead to complex configurations where fine tuning is needed to provide SH solutions. To contribute to enhancing the design and the assessment of such solutions for WS technology, we designed and implemented a monitoring and measurement framework, which is part of a larger Self-Healing Architectures (SHA) developed during the European WS-DIAMOND project. We implemented the Conference Management System (CMS), a real WS-based complex application. We achieved a large-scale experimentation campaign by deploying CMS on top of SHA on the French grid Grid5000. We experienced the problem as if we were a service provider who has to tune reconfiguration strategies. Our results are available on the web in a structured database for external use by the WS community. Copyright © 2010 John Wiley & Sons, Ltd. [source] 54 Benthic marine algal herbarium of long island sound digital collectionJOURNAL OF PHYCOLOGY, Issue 2003S. Cudiner The University of Connecticut presents the "Benthic Marine Algal Herbarium of Long Island Sound Digital Collection." The collection is available on the web for teaching and identification purposes. Phase One of this project will be finished later by early next year. Currently, the collection has approximately 60% of all Long Island Sound macroalgae species. The taxonomy is part of a collaboration between the University of Connecticut and the Northeast Algal Society (NEAS). Thus far, the specimens have come from Dr. Charles Yarish's herbarium and from the Environmental Laboratory at Millstone Power Station on Long Island Sound. The botanical illustrations are from "Illustrated Key to the Seaweeds of New England" by Martine Villalard-Bohnsack. Database features include the ability to create searches and generate sets based on subjects, division, class, order, family, genus, habitat, species, keyword, and location. Data retrieved includes JPG image, cataloged data, map regions, synonyms, and illustrated microscopic, cross section and surface view for some species. The web site is available for use at: http://www.algae.uconn.edu [source] Plasma Proteome Database as a resource for proteomics researchPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2005Babylakshmi Muthusamy Abstract Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778,distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein-coding regions were mapped onto the protein sequences. We found a number of examples of isoform-specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org. [source] | |||||||||||||