207751
PIDD: database for Protein Inter-atomic Distance Distributions
Protein Inter-atomic Distance Distributions (PIDD) is a dedicated database and structural bio-informatics system for distance based protein modeling. The database is developed to host and analyze the statistical data for protein inter-atomic distances based on their distributions in databases of known protein structures such as in the Protein Data Bank (PDB). PIDD is capable of generating, caching, and displaying the statistical distributions of the distances of various types and ranges. The collected information can be used to extract geometric restraints or mean-force potentials for protein structure determination including nuclear magnetic resonance structure determination and comparative model refinement. PIDD is supported with a friendly designed web interface so that users can easily specify the distance types and ranges, and retrieve, visualize or download the distributions of the distances as they desire. PIDD is freely accessible at
7810391
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints
The protein structures determined by NMR (Nuclear Magnetic Resonance Spectroscopy) are not as detailed and accurate as those by X-ray crystallography and are often underdetermined due to the inadequate distance data available from NMR experiments. The uses of NMR-determined structures in such important applications as homology modeling and rational drug design have thus been severely limited. Here we show that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures. We show through a survey on 462 NMR structures that, in fact, many inter-atomic distances in these structures deviate considerably from their database distributions and based on the refinement results on 10 selected NMR structures that these structures can actually be improved significantly when a selected set of distances are constrained within their high probability ranges in their database distributions.
26994753
Efficient Scheduling for Reducing Load in the IMS Presence Service
27854712
Retrieval of Multimedia Web Documents and Removal of Redundant Information
This paper describes a search engine for multimedia web documents and a methodology for removing (partially or totally) redundant information from multiple documents in an effort to synthesize new documents. In this paper, a typical multimedia document contains free text and images and additionally has associating well-structured data. An SQL-like query language, WebSSQL, is proposed to retrieve this type of documents. The main differences between WebSSQL and other proposed SQL extensions for retrieving web documents are that WebSSQL is similarity-based and supports conditions on images. This paper also deals with the detection and removal of redundant information (text paragraphs and images) from multiple retrieved documents. Documents reporting the same or related events and stories may contain substantial redundant information. The removal of the redundant information and the synthesis of these documents into a single document can not only save a user's time to acquire the information but also storage space to archive the data. The methodology reported here consists of techniques for analyzing text paragraphs and images as well as a set of similarity criteria used to detect redundant paragraphs and images. Examples are provided to illustrate these techniques.
44526903
Hamiltonicity, neighborhood intersections and the partially square graphs
Abstract Let G be a graph. The partially square graph G ∗ of G is a graph obtained from G by adding edges uv satisfying the conditions uv∉E(G), and there is some w∈N(u)∩N(v), such that N(w)⊆N(u)∪N(v)∪{u,v}. A non-negative rational sequence (a 1 ,a 2 ,…,a k+1 ) is called an LTW-sequence if the following conditions are satisfied: (1) a 1 ⩽1; (2) for arbitrary i 1 ,i 2 ,…,i h ∈{2,3,…,k+1},∑ j=1 h i j ⩽k+1 implies ∑ j=1 h (a i j −1)⩽1 . In this paper, we will use the technique of the vertex insertion on l -connected ( l=k,k−1 or k+1,k⩾2 ) graphs to provide a unified proof for G to be hamiltonian, traceable, 1 -hamiltonian or hamiltonian-connected, the sufficient conditions are expressed by weighted sums of the neighborhood intersections in G of independent sets in G ∗ , where the weights are LTW-sequences.
10943355
Constructing Interface Schemas for Search Interfaces of Web Databases
Many databases have become Web-accessible through form-based search interfaces (i.e., search forms) that allow users to specify complex and precise queries to access the underlying databases. In general, such a Web search interface can be considered as containing an interface schema with multiple attributes and rich semantic/meta information; however, the schema is not formally defined on the search interface. Many Web applications, such as Web database integration and deep Web crawling, require the construction of the schemas. In this paper, we introduce a schema model for complex search interfaces, and present a tool (WISE-iExtractor) for automatically extracting and deriving all the needed information to construct the schemas. Our experimental results on real search interfaces indicate that this tool is highly effective.
9755561
A Treemap-Based Result Interface for Search Engine Users
Search engines and metasearch engines on the World Wide Web typically display representative information such as the result document titles and snippets in a one-dimensional ranked list. Alternatively, a few others such as Clusty and Kartoo cluster their results so that users can, to a certain extent, interact with documents, keywords and/or clusters. The number of documents that can be effectively presented in one screen is usually limited to between 10 and 20. In this paper, we propose a method based on treemap visualization that substantially improve the information compactness. In addition, it provides a few unique post-search interaction methods that enable a user to manage a large number of results. An online prototype system is built. Various experiments are designed and done to evaluate the efficiency, effectiveness and usability.