Fragment Finder: a web-based software to identify similar three-dimensional structural motif

FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles (φ and ϕ). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling. The engine has facilities to view the resultant superposed or individual 3D structure(s) on the client machine. The proposed web server is made freely accessible at the following URL: or

SEO as a model of integrated digital marketing by using modern web technologies

Diploma thesis deals with extending the scope of search engine optimization (SEO) into integrated digital marketing model. A developed model is based on the use of modern web technologies to improve recognition and direct or indirect visibility of the website or web pages in both the search engines as well as digital media with natural or unpaid (organic or algorithmic) search results. The model is designed as a result of indetified shortcomings of a comprehensive approach to the presentation of micro, small and medium-sized businesses on the web and goes beyond the general SEO, which is presented as one of its components. Setting up a quality set of technical and creative elements to optimize the model is crucial to raise a website traffic. To display the concept of the model some practical steps are carried out and measured on the active webpage of a micro-enterprise. First, options and modes for technical, structural, design and content website optimization are presented, followed by analysis of the results, which allows identification of further improvement opportunities and determination of necessary steps. The result of diploma thesis is proven and scalable integrated digital marketing model based on the classical SEO approach. Semantic web, search engine advertising (SEA) and search engine marketing (SEM), which would more fully determine the scope of digital marketing, represent the opportunity for further discussions

SEO as a model of integrated digital marketing by using modern web technologies

Diploma thesis deals with extending the scope of search engine optimization (SEO) into integrated digital marketing model. A developed model is based on the use of modern web technologies to improve recognition and direct or indirect visibility of the website or web pages in both the search engines as well as digital media with natural or unpaid (organic or algorithmic) search results. The model is designed as a result of indetified shortcomings of a comprehensive approach to the presentation of micro, small and medium-sized businesses on the web and goes beyond the general SEO, which is presented as one of its components. Setting up a quality set of technical and creative elements to optimize the model is crucial to raise a website traffic. To display the concept of the model some practical steps are carried out and measured on the active webpage of a micro-enterprise. First, options and modes for technical, structural, design and content website optimization are presented, followed by analysis of the results, which allows identification of further improvement opportunities and determination of necessary steps. The result of diploma thesis is proven and scalable integrated digital marketing model based on the classical SEO approach. Semantic web, search engine advertising (SEA) and search engine marketing (SEM), which would more fully determine the scope of digital marketing, represent the opportunity for further discussions

QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure

QSCOP is a quantitative structural classification of proteins which distinguishes itself from other classifications by two essential properties: (i) QSCOP is concurrent with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and (ii) QSCOP covers the widely used SCOP classification with layers of quantitative structural information. The QSCOP-BLAST web server presented here combines the BLAST sequence search engine with QSCOP to retrieve, for a given query sequence, all structural information currently available. The resulting search engine is reliable in terms of the quality of results obtained, and it is efficient in that results are displayed instantaneously. The hierarchical organization of QSCOP is used to control the redundancy and diversity of the retrieved hits with the benefit that the often cumbersome and difficult interpretation of search results is an intuitive and straightforward exercise. We demonstrate the use of QSCOP-BLAST by example. The server is accessible at http://qscop-blast.services.came.sbg.ac.at

Search Engine Advertising Adoption and Utilization: An Empirical Investigation of Inflectional Factors

© Taylor & Francis Group, LLC. Search engine advertising (SEA) is a prominent source of revenue for search engine companies, and also a solution for businesses to promote their visibility on the web. However, there is little academic research available about the factors and the extent to which they may influence businesses’ decision to adopt SEA. Building on Theory of Planned Behavior, Technology Acceptance Model, and Unified Theory of Acceptance and Use of Technology, this study develops a context-specific model for understanding the factors that influence the decision of businesses to use SEA. Using structural equation modeling and survey data collected from 142 businesses, this research finds that the intention of businesses to use SEA is directly influenced by four factors: (i) attitude toward SEA, (ii) subjective norms, (iii) perceived control over SEA, and (iv) perceived benefits of SEA in terms of increasing web traffic, increasing sales and creating awareness. Furthermore, the research we discover six additional factors that have an indirect influence: (i) trust in search engines, (ii) perceived risk of SEA, (iii) ability to manage keywords and bids, (iv) ability to analyze and monitor outcomes, (v) advertising expertise, and (vi) using external experts

Assessment of forms and extent of tourism web promotion in Serbia

The subject of this paper is Web promotion of tourism in Serbia. Promotion was understood as one of the four basic elements of marketing on the Web. The paper analyses the main forms and the extent of use of Web tourism promotion. The focus is on domain characteristics, quality of presentation, visibility and search engine rank, Internet promotion techniques and number of visitors. Structural observation was the main method used to analyze 260 travel and tourism related websites in Serbia. However, as Serbia is in the process of political and economic transition, it is still characterized by insufficient technical development of the Internet and its low level of utilization by the tourism industry. Based on the obtained results the extent of use of Web tourism promotion in Serbia and its forms were assessed

WAQS : a web-based approximate query system

The Web is often viewed as a gigantic database holding vast stores of information and provides ubiquitous accessibility to end-users. Since its inception, the Internet has experienced explosive growth both in the number of users and the amount of content available on it. However, searching for information on the Web has become increasingly difficult. Although query languages have long been part of database management systems, the standard query language being the Structural Query Language is not suitable for the Web content retrieval. In this dissertation, a new technique for document retrieval on the Web is presented. This technique is designed to allow a detailed retrieval and hence reduce the amount of matches returned by typical search engines. The main objective of this technique is to allow the query to be based on not just keywords but also the location of the keywords within the logical structure of a document. In addition, the technique also provides approximate search capabilities based on the notion of Distance and Variable Length Don\u27t Cares. The proposed techniques have been implemented in a system, called Web-Based Approximate Query System, which contains an SQL-like query language called Web-Based Approximate Query Language. Web-Based Approximate Query Language has also been integrated with EnviroDaemon, an environmental domain specific search engine. It provides EnviroDaemon with more detailed searching capabilities than just keyword-based search. Implementation details, technical results and future work are presented in this dissertation

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Background: Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl webcite. Conclusions: RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field

An approximate search engine for structure

As the size of structural databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute-value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. In this dissertation, efficient search techniques are presented for retrieving trees from a database that are similar to a given query tree. Rooted ordered labeled trees, rooted unordered labeled trees and free trees are considered. Ordered labeled trees are trees in which each node has a label and the left-to-right order among siblings matters. Unordered labeled trees are trees in which the parent-child relationship is significant, but the order among siblings is unimportant. Free trees (unrooted unordered trees) are acyclic graphs. These trees find many applications in bioinformatics, Web log analysis, phyloinformatics, XML processing, etc. Two types of similarity measures are investigated: (i) counting the mismatching paths in the query tree and a data tree, and (ii) measuring the topological relationship between the trees. The proposed approaches include storing the paths of trees in a suffix array, employing hashing techniques to speed up retrieval, and counting the number of up-down operations to move a token from one node to another node in a tree. Various filters for accelerating a search, different strategies for parallelizing these search algorithms and applications of these algorithms to XML and phylogenetic data management are discussed. The proposed techniques have been implemented into a phylogenetic search engine which is fully operational and is available on the World Wide Web. Experimental results on comparing the similarity measures with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate the effectiveness of the search engine. Future work includes extending the techniques to other structural data, as well as developing new filters and algorithms for speeding up searching and mining in complex structures