Statistical analysis of amino acids in the vicinity of carbohydrate residues performed by GlyVicinity

Methods in Molecular Biology
Miguel A Rojas-Macias, Thomas Lütteke

Abstract

Protein-carbohydrate interactions are involved in various essential biological events. 3D structural data from the Protein Data Bank (PDB) can help to understand the molecular basis of the specificity of carbohydrate recognition by proteins. Such interactions can be analyzed statistically using GlyVicinity. This chapter exemplifies the usage of this tool to find information on the frequency of the occurrence of specific amino acids in the vicinity of individual carbohydrate residues and to analyze the type of interacting atoms and their spatial distribution around the glycans.

Citations

Jun 24, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Vojtěch Spiwok
Dec 14, 2017·Quarterly Reviews of Biophysics·Ruiyan ZhangHans-Christian Siebert
Jul 16, 2019·Methods : a Companion to Methods in Enzymology·Camille BesançonStéphanie Baud
Oct 7, 2021·PLoS Computational Biology·Daniel E Mattox, Chris Bailey-Kellogg

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