5856173
SHEETSPAIR: A Database of Amino Acid Pairs in Protein Sheet Structures
Within folded strands of a protein, amino acids (AAs) on every adjacent two strands form a pair of AAs. To explore the interactions between strands in a protein sheet structure, we have established an Internet-accessible relational database named SheetsPairs based on SQL Server 2000. The database has collected AAs pairs in proteins with detailed information. Furthermore, it utilizes a non-freetext database structure to store protein sequences and a specific database table with a unique number to store strands, which provides more searching options and rapid and accurate access to data queries. An IIS web server has been set up for data retrieval through a custom web interface, which enables complex data queries. Also searchable are parallel or anti-parallel folded strands and the list of strands in a specified protein.
445053
Prediction of Helix, Strand Segments from Primary Protein Sequences by a Set of Neural Networks
In prediction of secondary structure of proteins there are always some suspected segments. These suspected segments confuse people and lower the accuracy of prediction methods. To deal with this problem, a set of neural networks (NNs) are built based on helix, strand and coil segments selected from PDB. The test performance of these NNs on training data is perfect without surprise. However the prediction on test data is not good enough because the training data are lake of great representativeness. The results support the fact that closer neighbor vectors have the similar outputs of NNs. One can improve representativeness of training data without enlarging data scale as long as select less data from dense region and more from sparse region on condition that distribution of sample data has been known.
5382663
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
BackgroundQuantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics.ResultsWe have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling.ConclusionThe Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field.
16171710
An Analysis Framework of Factors Influencing China Software and Information Service Offshore Outsourcing
Offshore outsourcing has become popular because of cost or skill advantage. China is considered as one of major global software and information service offshore destinations, but it cannot compete with India right now. Based on literature review, this paper first presents an overview of the industry. Then 38 service providers in China are investigated to give a firm-level analysis of the industry. A framework of factors influencing the industry is presented. Influence factors are classified into macro factors, middle factors, and micro factors, each of which is analyzed in detail. It is concluded that China software and information service offshore outsourcing industry is of great potential, but needs marketing and advertising.
23948133
Building Domain Ontology Based on Web Data and Generic Ontology
The automatic or semi-automatic construction of ontology has become a research topic of interest in recent years. This paper describes a mechanism for constructing domain specific ontologies automatically based on web data and generic ontology. Firstly, we employ the hierarchical agglomerative clustering(HAC) algorithm, clustering web pages hierarchically and resulting in a binary tree. Then an algorithm is proposed, which selectd from the binary tree the significative nodes as topics implying concepts of domain interests. Lastly, the Chinese generic ontology, HowNet, is introduced to evolve the topics (together with their hierarchical structures) into domain ontology. We experiment our method in the field of computer hardware based on web pages collected from Chinese BtoC web sites. An in-depth discussion on the experiment results is also given.
39605083
RSA-based Verifiable and Recoverable Encryption of Signatures and its application in certified e-mail delivery
This paper presents two variant protocols RSA-CEMDI and RDA-CEMD2 for certified e-mail delivery with RSA receipts. The protocols provide non-repudiation of origin and non-repudiation of receipt security services to protect communicating parties from each other's false denials that the e-mail message has been sent and received. The protocols also provide strong fairness to ensure that the recipient receives the e-mail if and only if the sender receives the receipt. Services of an off-time and transparent third party are invoked in the protocols only in exceptional circumstances, i.e.. when the communicating parties fail to complete the e-mail for receipt exchange due to a network failure or a party's misbehaviour. Protocol RSA-CEMDI also offers confidentiality protection for the e-mail message and the corresponding receipt from the third party, achieved at the cost of some additional computations. The protocols are based on a cryptographic primitive called Verifiable and Recoverable Encryption of a Signature (VRES). The novel design of the VRES allows efficiency improvements in comparison with the related certified e-mail delivery protocols based on similar primitives.
16577876
FAME: Adding Multi-Level Authentication to Shibboleth
The paper describes the design of FAME (Flexible Access Middleware Extension) architecture aimed at providing multi-level user authentication service for Shibboleth, which is endorsed by the Joint Information Systems Committee (JISC) as the next generation authentication and authorisation infrastructure for the UK Higher Education community. FAME derives authentication assurance level based upon the strength of the authentication token and protocol used by the user when authenticating and feeds it to the PERMIS authorisation decision engine via Shibboleth to enable more fine-grained access control. In this way, access to resources is controlled according to the strength of the authentication method so that more sensitive resources may require users to identify themselves using a higher level of authentication.