Thomas Lütteke

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This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new(More)
The development of glycan-related databases and bioinformatics applications is considerably lagging behind compared with the wealth of available data and software tools in genomics and proteomics. Because the encoding of glycan structures is more complex, most of the bioinformatics approaches cannot be applied to glycan structures. No standard procedures(More)
Knowledge of the 3D structure of glycoproteins and protein-carbohydrate complexes is indispensable to fully understand the biological processes they are involved in. Carbohydrate Structure Suite is an attempt to automatically analyse carbohydrate structures contained in the PDB and make the results publicly available on the internet. Characteristic torsion(More)
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(More)
Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current(More)
The development of glycan related databases and bioinformatics applications is considerably lagging behind compared with the wealth of available data and software tools in genomics and proteomics. Since the encoding of glycan structures is more complex, most of the bioinformatics approaches cannot be applied to glycan structures. No standard procedures(More)
Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to(More)
Symbol Nomenclature for Graphical Representations of Glycans Ajit Varki1,2,3, Richard D Cummings1,2,4,5,6, Markus Aebi1,2,7, Nicole H Packer1,2,8, Peter H Seeberger1,2,9, Jeffrey D Esko1,3, Pamela Stanley1,10, Gerald Hart1,11, Alan Darvill1,12, Taroh Kinoshita1,13, James J Prestegard1,12, Ronald L Schnaar1,11, Hudson H Freeze14,15, Jamey D Marth14,16,(More)
Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on(More)
The frequency of glycosylated protein 3D structures in the Protein Data Bank (PDB) is significantly lower than the proportion of glycoproteins in nature, and if glycan 3D structures are present, then they often exhibit a large degree of errors. There are various reasons for this, one of which is a comparably low support of carbohydrates in software tools(More)