A5088409948- Glycosylation and Glycoproteins Research
- Carbohydrate Chemistry and Synthesis
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolites in Food Biotechnology
- Protein Structure and Dynamics
- Galectins and Cancer Biology
- Biomedical Text Mining and Ontologies
- Antimicrobial Peptides and Activities
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Immune Response and Inflammation
- Immune cells in cancer
- RNA and protein synthesis mechanisms
- Enzyme Production and Characterization
- Biofuel production and bioconversion
- Scientific Computing and Data Management
- Ubiquitin and proteasome pathways
- Cytokine Signaling Pathways and Interactions
- Advanced Proteomics Techniques and Applications
- interferon and immune responses
- Escherichia coli research studies
- Machine Learning in Bioinformatics
- Seaweed-derived Bioactive Compounds
- Supramolecular Self-Assembly in Materials
Justus-Liebig-Universität Gießen
2014-2024
Ludwig-Maximilians-Universität München
2017
International Union of Pure and Applied Chemistry
2015
University of Georgia
2014
Macquarie University
2014
Niigata University
2014
National Institute of Advanced Industrial Science and Technology
2014
Noguchi Institute
2014
Research Organization of Information and Systems
2014
Soka University
2014
Author(s): Varki, Ajit; Cummings, Richard D; Aebi, Markus; Packer, Nicole H; Seeberger, Peter Esko, Jeffrey Stanley, Pamela; Hart, Gerald; Darvill, Alan; Kinoshita, Taroh; Prestegard, James J; Schnaar, Ronald L; Freeze, Hudson Marth, Jamey Bertozzi, Carolyn R; Etzler, Marilynn E; Frank, Martin; Vliegenthart, Johannes Fg; Lutteke, Thomas; Perez, Serge; Bolton, Evan; Rudd, Pauline; Paulson, James; Kanehisa, Minoru; Toukach, Philip; Aoki-Kinoshita, Kiyoko F; Dell, Anne; Narimatsu, Hisashi;...
This report presents the conclusions of X-ray Validation Task Force worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation deposited structures were adopted, allowing a much more sophisticated understanding all components macromolecular crystals. size creates new opportunities to validate by comparison with existing database, and now-mandatory deposition structure factors underlying diffraction data. These developments highlighted need...
Abstract The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It hosted by National Center Biotechnology Information (NCBI) at NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to SNFG page in past year update rules depicting SNFG, include more examples use, particularly non-mammalian organisms,...
Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate prediction, determination, design. In this work, we developed a glycan-modeling algorithm, GlycanTreeModeler, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) common glycan conformations derived from data the Protein Data Bank (PDB) quantum...
Knowledge of the 3D structure glycoproteins and protein–carbohydrate complexes is indispensable to fully understand biological processes they are involved in. Carbohydrate Structure Suite an attempt automatically analyse carbohydrate structures contained in PDB make results publicly available on internet. Characteristic torsion angles, glycoprotein sequences carbohydrate–protein interactions analysed. Furthermore, tools crosslink databases check integrity included. The service at (...
Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have large pharmaceutical diagnostic potential. Knowledge the 3D structure glycans is prerequisite for complete understanding their functions. The largest source biomolecular structures Protein Data Bank. However, about 30% all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors glycan description. Unfortunately, no software currently...
The EUROCarbDB project is a design study for technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology glycomic research. relational database containing glycan structures, their biological context and, when available, primary interpreted analytical data from high-performance liquid chromatography, mass spectrometry nuclear magnetic resonance experiments. Database content can be accessed via web-based user...
Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation structure analysis then calls software since adding meaning to large data collections reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on function glycans, their interaction with proteins or enzymatic synthesis. However, this is partial, scattered...
Glycosciences.DB, the glycan structure database of Glycosciences.de portal, collects various kinds data on structures, including carbohydrate moieties from worldwide Protein Data Bank (wwPDB) structures. This way it forms a bridge between glycomics and proteomics resources. A major update this combines redesigned web interface with series new functions. These include separate entry pages not only for structures but also literature references wwPDB entries, improved substructure search...
Knowledge of the three-dimensional structures carbohydrate molecules is indispensable for a full understanding molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) valuable resource structural information on glycoproteins and complexes. Unfortunately, many carbohydrate moieties PDB contain inconsistencies errors. This article gives an overview that can be obtained from individual entries...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Abstract Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created released to public. Unfortunately, there is no common standard in representation of stored information or a machine-readable interface allowing groups easily extract cross-reference information. Results: An international group experts field glycomics worked together create Resource Description Framework (RDF) for data, focused on glycan sequences related biological...
Abstract
Conformational energy maps of the glycosidic linkages are a valuable resource to gain information about preferred conformations and flexibility carbohydrates. Here we present GlycoMapsDB, new database containing more than 2500 calculated conformational for variety di- pentasaccharide fragments contained in N- O-glycans. Oligosaccharides representing branchpoints N-glycans included set fragments, thus influence neighbouring residues is reflected maps. During refinement crystal structures,...
Abstract Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans) , which can, for example, serve “switches” that toggle between different functions of glycoprotein or glycolipid. Due to the advancement glycomics technologies are used characterize glycan structures, many databases now publicly available and provide useful information glycoscience research. However, these have almost no link other life science databases. Results In order...
Escherichia coli O-antigen database (ECODAB) is a web-based application to support the collection of E. structures, polymerase and flippase amino acid sequences, NMR chemical shift data O-antigens as well information on glycosyltransferases (GTs) involved in assembly polysaccharides. The content has been compiled from scientific literature. Furthermore, system evolved being repository one that can be used for generating novel its own. GT specificity suggested through sequence comparison with...
Abstract Nonulosonic acids or non-2-ulosonic (NulOs) are an ancient family of 2-ketoaldonic (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in 3-deoxy form (referred to as “sialic acids”) 3,9-dideoxy “sialic-acid-like” form. The former sialic most common the deuterostome lineage, including vertebrates, and mimicked by some their pathogens. latter sialic-acid-like molecules found bacteria archaea. NulOs often prominently positioned at outermost...
Abstract Carbohydrates and glycoproteins modulate key biological functions. Computational approaches inform function to aid in carbohydrate structure prediction, determination, design. However, experimental determination of sugar polymers is notoriously difficult as glycans can sample a wide range low energy conformations, thus limiting the study glycan-mediated molecular interactions. In this work, we expanded RosettaCarbohydrate framework, developed benchmarked effective tools for glycan...