Bioinformatics For Glycobiology And Glycomics

This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology. The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates. Key features: Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation. Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures. Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank. Assumes only a basic knowledge of biology and bioinformatics.

A Focused, State-of-the-Art Overview of This Evolving Field Presents Various Techniques for Glycoinformatics The development and use of informatics tools and databases for glycobiology and glycomics research have increased considerably in recent years. In addition to accumulating well-structured glyco-related data, researchers have now developed semi-automated methods for the annotation of mass spectral data and algorithms for capturing patterns in glycan structure data. These techniques have enabled researchers to gain a better understanding of how these complex structures affect protein function and other biological processes, including cancer. One of the few up-to-date books available in this important area, Glycome Informatics: Methods and Applications covers all known informatics methods pertaining to the study of glycans. It discusses the current status of carbohydrate databases, the latest analytical techniques, and the informatics needed for rapid progress in glycomics research. Providing an overall understanding of glycobiology, this self-contained guide focuses on the development of glycome informatics methods and current problems faced by researchers. It explains how to implement informatics methods in glycobiology. The author includes the required background material on glycobiology as well as the mathematical concepts needed to understand advanced mining and algorithmic techniques. She also suggests project themes for readers looking to begin research in the field.

The Handbook of Glycomics provides the first comprehensive overview of the emerging field of glycomics, defined as the study of all complex carbohydrates in an organism or cell ("the glycome"). Beginning with analytic approaches and bioinformatics, this work provides a detailed discussion of relevant databases, data integration, and analysis. It then moves on to a discussion of specific model organism and pathogen glycomes followed by therapeutic approaches to human disorders of glycosylization. Structure and function of glycomes are included along with state-of-the-art technologies and systems approaches to the analysis of glycans. Synthesizes contributions from experts in biology, chemistry, bioinformatics, biotechnology, and medicine Highlights chapters devoted to chemical synthesis, cancer glycomics and immune cell glycomics Includes discussions of proteomics, mass spectrometry, NMR, array technology, and transcriptomics analytic approaches

This book provides glycoscientists with a handbook of useful databases that can be applied to glycoscience research. Although many databases are now publicly available, one of the hurdles for their users is the learning curve required to effectively utilize those databases. Therefore, this book not only describes the existing databases, but also provides tips on how to obtain the target data. That is, because many databases provide a variety of data that could be obtained from different perspectives, each chapter provides users with potential biological questions that can be answered by a particular database and step-by-step instructions, with figures, on how to obtain that data. Troubleshooting tips are also provided to aid users encountering problems that can be predicted when using these databases. Moreover, contact information for each database is provided in case unexpected issues arise.

Over the past decade, the scientific community of post-proteomics and post-genomics witnessed the rapid evolution of a new scientific field - the glycomics. The investigation of both glycans and glycan-binding proteins and lipids revealed increasingly the role of complex carbohydrates in diverse inter- and intracellular processes. Advances in analytical technologies, carbohydrate chemistry and structural biology led to an increased understanding of the high degree of variability of both composition, structure and function of sugars. Additionally, structure-function studies showed an inherent complexity which is determined by different branching patterns, various possible linkage positions and numerous building blocks. Even though there has been significant progress in the development of interdisciplinary approaches such as experimental and computer scientific tools, the general technological developments in glycomics lag behind those in the proteomic and genomic areas. In particular, despite the current progress in glyco-bioinformatics regarding the computational characterization of carbohydrates, the glycomics community is still lacking a systematic and comprehensive database and analysis software. The database landscape is made up of numerous independent and disconnected databases with partially overlapping core areas. These databases provide neither complete nor compatible data sets on glycan structures. Additionally, since the individual data encoding and analysis software tools do not use a common language for the representation of schematic structures and sequence topologies, data processing and interpretation become extremely challenging. The underlying aim of this symposium is to bring together glycochemists and biologists with experts in bioinformatics and computer sciences to pave the way for a concerted effort in the area of glyco-bioinformatics. Scientists who "produce" data met those who "use" the data. They discussed aspects such as data mining, structure prediction and docking of carbohydrates, as well as web-based services to combine proteomics and glycomics data for structure-function research and glycosylation analysis. This meeting continued successfully the efforts resulting from the first symposium held in October 2009 to discuss the necessity of a uniform data reporting practice that supports biologists, chemists and all interested in glycosciences to enable the integration of their experimental and analysis data into glyco-bioinformatics platforms.

A new focus on glycoscience, a field that explores the structures and functions of sugars, promises great advances in areas as diverse as medicine, energy generation, and materials science, this report finds. Glycans--also known as carbohydrates, saccharides, or simply as sugars--play central roles in many biological processes and have properties useful in an array of applications. However, glycans have received little attention from the research community due to a lack of tools to probe their often complex structures and properties. Transforming Glycoscience: A Roadmap for the Future presents a roadmap for transforming glycoscience from a field dominated by specialists to a widely studied and integrated discipline, which could lead to a more complete understanding of glycans and help solve key challenges in diverse fields.

This book provides current glycoinformatics methods and protocols used to support the determination of carbohydrate structures in biological samples as well as carbohydrate structure databases, the interaction of carbohydrates with proteins, and theoretical and experimental methods to study their three-dimensional structure and dynamics. Glycoinformatics explores this recently emerged field, which has come into being in order to address the needs of encoding, storing, and analyzing carbohydrate ‘sequences’ and their taxonomy using computers. Written in the highly successful Methods in Molecular Biology series format, chapters contain the kind of detailed description and key implementation advice to ensure successful results. Authoritative and timely, Glycoinformatics demonstrates the progress that has been achieved in glycoinformatics, which indicates that it is no longer a niche subject covered by only a few scientists but is truly coming of age.

The Beilstein Symposia address contemporary issues in the chemical and related sciences by employing and interdisciplinary approach. Scientists from a wide range of areas are invited to present aspects of their work for discussion, with the aim of not only advancing sciences, but also enhancing interdisciplinary communication. Traditionally, the Beilstein Symposia are kept small with up to 50 participants to provide a convivial atmosphere for the both lectures and lively discussions and the ready exchange of thoughts and ideas. The appreciation and understanding of the role that carbohydrates play in nature has grown over the last few years driven by the advances in our ability to analyze and synthesize their structures. Their role not only as primary energy-storage molecules but also as structural modifiers of e.g. glycoproteins and glycolipids, as well as in physiological and pathological events such as adherence, cell-cell interaction, transport, signaling and protection is becoming clearer and more accessible to researchers. Over the last decade the fields of glycobiology and glycochemistry in combination with in-silico applications have been augmented by a further field - glycomics. A major aim of glycomics research is to achieve a comprehensive identification and characterization of the repertoire of glycan structures present in an organism, cell or tissue at a defined time. The continual improvement of analysis methods and computational techniques leads to glycan characterization and identification with increased depth, speed and efficiency but also generates ever increasing amounts of data of variable quality and completeness. Thus the many web-accessible repositories result in a highly fragmented knowledgebase which in consequence complicates the development and application of bioinformatics tools for the analysis of this data. This situation has led to a general consensus that community wide efforts should be spent towards consolidating and systematizing the collective knowledgebase with integration of universal bioinformatics tools for both the representation, mining as well as annotation of experimental data sets to advance and interface glycomics with related genomics and proteomics projects. Additionally, both experimentalists and bioinformaticians also expressed their demands for data reporting practices that include the comprehensive description of conditions, techniques and experimental results to enable researchers to evaluate the degree of structural definitions, to interpret the results and to reproduce the experiments. This 3rd Beilstein Glyco-Bioinformatics Symposium brought together those scientists that produce data with those that use the data and make it available to the community. In particular, in their presentations speakers delivered insights into the diverse physiological and structural subtleties of sugars by covering aspects such as: structure-function relationships of carbohydrates, modeling carbohydrate structure and carbohydrate interactions with other biomacromolecules, deciphering carbohydrate signals, carbohydrate identification, annotation and analysis, metadata for the description of glycomics experiments, software tools for data mining and analysis.