Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Keywords: THERAPIES ; radiation therapy ; MOVEMENT ; THERAPY ; LUNG ; radiotherapy ; radiation ; SIMULATION ; ELEMENT ; TARGET ; RADIATION-THERAPY
    Type of Publication: Book chapter
    Signatur Availability
    BibTip Others were also interested in ...
  • 2
    Keywords: ENVIRONMENT ; CELL ; Germany ; DISEASE ; TIME ; BASE ; CONTRAST ; SEQUENCE ; TARGET ; PATTERNS ; DESIGN ; DIFFERENCE ; ESCHERICHIA-COLI ; DATABASE ; VACCINES ; EVOLUTION ; ADHESION ; STATISTICAL-ANALYSIS ; STRATEGIES ; REVEALS ; TARGETS ; ARCHITECTURE ; OLIGOSACCHARIDES ; FEATURES ; RE ; PATTERN ; databases ; LEVEL ; analysis ; lipopolysaccharide ; ENGLAND ; comparison ; modification ; bacterial ; mammals
    Abstract: Background: There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance. Results: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than tenfold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties. Conclusion: For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans
    Type of Publication: Journal article published
    PubMed ID: 18694500
    Signatur Availability
    BibTip Others were also interested in ...
  • 3
    Keywords: Germany ; IMAGES ; MOLECULE ; molecular ; RE ; LIBRARY ; MOLECULAR-STRUCTURE ; BIOLOGICAL MACROMOLECULES ; VIEWER
    Abstract: Using a web browser without additional software and generating interactive high quality and high resolution images of bio-molecules is no longer a problem. Interactive visualization of 3D molecule structures by Internet browsers normally is not possible without additional software and the disadvantage of browser-based structure images ( e. g. by a Java applet) is their low resolution. Scientists who want to generate 3D molecular images with high quality and high resolution ( e. g. for publications or to render a molecule for a poster) therefore require separately installed software that is often not easy to use. The alternative concept is an interactive server-side rendering application that can be interfaced with any web browser. Thus it combines the advantage of the web application with the high-end rendering of a raytracer. This article addresses users who want to generate high quality images from molecular structures and do not have software installed locally for structure visualization. Often people do not have a structure viewer, such as RasMol or Chime ( or even Java) installed locally but want to visualize a molecule structure interactively. AISMIG ( An Interactive Server-side Molecule Image Generator) is a web service that provides a visualization of molecule structures in such cases. AISMIG-URL: http://www.dkfz-heidelberg.de/spec/aismig/
    Type of Publication: Journal article published
    PubMed ID: 15980568
    Signatur Availability
    BibTip Others were also interested in ...
  • 4
    Keywords: SPECTRA ; evaluation ; Germany ; ALGORITHM ; SAMPLE ; COMPONENTS ; MOLECULES ; TIME ; IMPACT ; IONS ; BIOLOGY ; MOLECULAR-BIOLOGY ; SIGNAL ; MOLECULE ; CLEAVAGE ; COMPONENT ; mass spectrometry ; fragmentation ; DATABASE ; PRODUCT ; DE-NOVO ; PROTEOMICS ; OLIGOSACCHARIDES ; MASSES ; molecular biology ; molecular ; PRODUCTS ; SOFTWARE ; ANNOTATION ; glycans ; analysis ; methods ; technique ; SIGNALS ; FRAGMENT ; SPECTRUM ; ACCESS ; SET ; - ; modification ; (semi-)automated annotation ; backtracking algorithm ; freely available software ; glycan composition analysis ; GLYCOBIOLOGY RESEARCH ; INFRARED MULTIPHOTON DISSOCIATION ; MS SPECTRA
    Abstract: Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, the lack of robust, dependable, and freely available software for the (semi-) automatic annotation of mass spectra is still a severe bottleneck that hampers their rapid interpretation. In this article the" Glyco-Peakfinder" web-service is described allowing de novo determination of glycan compositions from their mass signals. Starting from a basic set of mandatory masses of glycan components, the calculation can be performed without any knowledge concerning the biological background of the sample or the fragmentation technique used. "Glyco-Peakfinder" assigns all types of fragment ions including monosaccharide cross-ring cleavage products and multiply charged ions. It provides full user control to handle modified glycans (persubstituted molecules, reducing-end modifications, glycoconjugates) and ion types. The formula applied to calculate the fragment masses and an outline of the implemented algorithm are discussed. A systematic evaluation of the dependence of all factors influencing the computation time revealed strikingly different impact of the individual calculation steps. To provide access to known carbohydrate structures a "composition search" in the open access database GLYCOSCIENCES.de can be performed. The service is available at the URL: www.eurocarbdb.org/applications/ms-tools
    Type of Publication: Journal article published
    PubMed ID: 18072204
    Signatur Availability
    BibTip Others were also interested in ...
  • 5
    Keywords: Germany ; BIOLOGY ; DUPLICATION ; glycomics ; KEGG
    Abstract: Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at http://www.glyco.ac.ru/bcsdb/ and the GLYCOSCIENCES.de portal at http://www.glycosciences.de/
    Type of Publication: Journal article published
    PubMed ID: 17202164
    Signatur Availability
    BibTip Others were also interested in ...
  • 6
    Keywords: COMBINATION ; COMPLEX ; BIOLOGY ; MOLECULAR-BIOLOGY ; LINKAGE ; ACID ; NUMBER ; DERIVATIVES ; DIVERSITY ; OLIGOSACCHARIDES ; solid-phase synthesis ; GLYCOSIDES ; molecular biology ; molecular ; CHAIN ; assembly ; PH ; glycans ; analysis ; SIZE ; USA ; UNIT ; ACCESS ; SET ; CHEMICAL SYNTHESIS ; block ; AUTOMATED SYNTHESIS ; HEXASACCHARIDE ; OLIGOSACCHARIDE SYNTHESIS ; PROTECTING-GROUP
    Abstract: The diversity of three major classes of mammalian carbohydrates, mainly glycotipids and O- and N-linked glycans, deposited in the databank GLYCOSCIENCES.de was subjected to statistical analyses. Size, chain length, and branching complexity were accessed and revealed that the average oligosaccharide is composed of about eight monosaccharide units. About a quarter of all oligosaccharides are strictly linear, and the remainder are branched at least once. Glucosamine, galactose, and mannose are dominating and comprise 75% of the monosaccharides within mammalian oligosaccharicle frameworks. alpha-linked sialic acid, alpha-linked fucose, and P-linked galactose decorate the majority of reducing termini. Glucose as the most abundant carbohydrate in mammals plays only a very minor role within these structures. Particular emphasis was placed on analyzing the way the monosaccharide units are linked within the oligomeric framework. just 11 monosaccharide connections account for 〉75% of all linkages. Thus, the number of structural combinations found in nature, the part of the occupied mammalian glycospace, is much smaller than expected. As a result, a potential set of building blocks for oligosaccharicle assembly is presented. This potential building block set was correlated with the accessible 3299 mammalian carbohydrate structures in the GLYCOSCIENCES.de databank. Only 36 building blocks are required to construct 75% of the 3299 mammalian oligosaccharides
    Type of Publication: Journal article published
    PubMed ID: 18041818
    Signatur Availability
    BibTip Others were also interested in ...
  • 7
    Keywords: Germany ; COMPLEX ; primary ; BIOLOGY ; MOLECULAR-BIOLOGY ; SEQUENCE ; SEQUENCES ; DATABASE ; PROJECT ; NOMENCLATURE ; molecular biology ; molecular ; CHEMISTRY ; FEATURES ; RE ; VARIANT ; databases ; XML ; ENGLAND ; glycobioinformatics ; modeling ; block ; BIOLOGICAL SOURCES ; carbohydrate sequence format ; CURATED RELATIONAL DATABASE ; GLYCOPROTEIN GLYCAN STRUCTURES ; GLYCOSUITEDB ; structure encoding
    Abstract: As part of the EUROCarbDB project (www.eurocarbdb.org) we have carefully analyzed the encoding capabilities of all existing carbohydrate sequence formats and the content of publically available structure databases. We have found that none of the existing structural encoding schemata are capable of coping with the full complexity to be expected for experimentally derived structural carbohydrate sequence data across all taxonomic sources. This gap motivated us to define an encoding scheme for complex carbohydrates, named GlycoCT, to overcome the current limitations. This new format is based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics. (C) 2008 Published by Elsevier Ltd
    Type of Publication: Journal article published
    PubMed ID: 18436199
    Signatur Availability
    BibTip Others were also interested in ...
  • 8
    Keywords: PROTEIN ; SEQUENCES ; PROTEIN DATA-BANK
    Abstract: GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank, which renders the database currently the most comprehensive and unified resource for carbohydrate structures worldwide. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases. The complete database can be downloaded freely or accessed through a Web-interface (www.glycome-db.org) that provides flexible and powerful search functionalities
    Type of Publication: Journal article published
    PubMed ID: 21045056
    Signatur Availability
    BibTip Others were also interested in ...
  • 9
    Keywords: Germany ; MODEL ; GENE ; GENES ; GENOME ; PROTEIN ; PROTEINS ; COMPLEX ; COMPLEXES ; DNA ; BIOLOGY ; SEQUENCE ; SEQUENCES ; DATABASE ; bioinformatics ; NOMENCLATURE ; INTEGRATION ; review ; RE ; databases ; SOFTWARE ; ANNOTATION ; RESOURCE ; methods ; RESOURCES ; NOR ; microbiology ; ENGLAND ; biotechnology ; GENOMES ; bacterial ; biological ; CONSORTIUM ; BIOLOGICAL SOURCES ; CURATED RELATIONAL DATABASE ; GLYCOPROTEIN GLYCAN STRUCTURES ; GLYCOSUITEDB ; structure encoding ; GLYCOSCIENCES.DE
    Abstract: Background: Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results: We have implemented procedures which download the structures contained in the seven major databases, e. g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion: GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource
    Type of Publication: Journal article published
    PubMed ID: 18803830
    Signatur Availability
    BibTip Others were also interested in ...
  • 10
    Keywords: NMR-SPECTROSCOPY ; glycosylation ; databases ; PROTEIN DATA-BANK ; GLYCOBIOLOGY RESEARCH ; BIOLOGICAL SOURCES ; CURATED RELATIONAL DATABASE ; GLYCOPROTEIN GLYCAN STRUCTURES ; N-GLYCANS ; CARBOHYDRATE SEQUENCES ; DESORPTION/IONIZATION MASS-SPECTROMETRY ; glycoinformatics ; informatics tools ; open-source
    Abstract: The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb
    Type of Publication: Journal article published
    PubMed ID: 21106561
    Signatur Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...