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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)
BACKGROUND Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the(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 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)
BACKGROUND Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now(More)
Glycans are among the most complex biological molecules found in nature, being composed of monosaccharide units in various combinations and linkages, and featuring diverse and asymmetric types of branching. Until the 1970s, glycan structures were generally represented in scientific publications as chemically accurate drawings, or using standard(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)
MOTIVATION Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored(More)