Analyzing Glycan Structure Synthesis with the Glycan Pathway Predictor (GPP) Tool

Abstract

This chapter describes the Glycan Pathway Predictor Tool, which is available as a part of the RINGS (Resource for INformatics of Glycomes at Soka) website at http://www.rings.t.soka.ac.jp/. It implements the mathematical model of N-glycosylation previously described by Krambeck et al. (Glycobiology 19:1163–1175, 2009). This tool computes the glycans that can be potentially generated from a select set of glyco-enzymes, based on a mathematical model that characterizes substrate specificity. The resulting glycans are displayed as a pathway map, which can be evaluated in an interactive manner. Detailed results can also be obtained for each glycan that is theoretically generated, along with the corresponding enzymes that were found to be involved with the selected glycan. Thus, glycobiologists can take a particular starting glycan structure as input, select a set of glyco-enzymes, and instantly retrieve the set of potentially synthesized glycans as a pathway map or as a text file. Applications of this tool are numerous, including prediction of glycan profiles for a glyco-gene knockout experiment, comparison with mass spectrometric data, etc.