Summary
The 3D structural data of glycoprotein or protein-carbohydrate complexes that are found in the Protein Data Bank (PDB) are an interesting data source for glycobiologists. Unfortunately, carbohydrate components are difficult to find with the means provided by the PDB. The GLYCOSCIENCES.de internet portal offers a variety of tools and databases to locate and analyze these structures. This chapter describes how to find PDB entries that feature a specific carbohydrate structure and how to locate carbohydrate residues in a 3D structure file and to check their consistency. In addition to this, methods to statistically analyze torsion angles and the abundance of amino acids both in the neighborhood of glycosylation sites and in the spatial vicinity of non-covalently bound carbohydrate chains are summarized.
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Acknowledgment
The authors thank Dr Robin Thomson, Institute for Glycomics, Griffith University, Australia for carefully reading the manuscript, testing the applications and many useful suggestions to improve its readability. The development of GLYCOSCIENCES.de at the German Cancer Research Center was supported by a Research Grant of the German Research Foundation (DFG BIB 46 HDdkz 01-01) within the digital library program.
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Lütteke, T., von der Lieth, C.W. (2009). Data Mining the PDB for Glyco-Related Data. In: Packer, N.H., Karlsson, N.G. (eds) Glycomics. Methods in Molecular Biology™, vol 534. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-022-5_21
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DOI: https://doi.org/10.1007/978-1-59745-022-5_21
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