The article outlines the history, capabilities, and significance of Privateer, a specialized carbohydrate validation software used in structural biology.
The determination of the atomic structures of glycoproteins is uniquely challenging, even though the glycans themselves are only moderate in size. Privateer was originally created to mine monosaccharides and their structural contexts from the Protein Data Bank (PDB). Over the past decade, it has evolved into a ubiquitous tool in carbohydrate model building. It automatically detects errors in sugar stereochemistry, regiochemistry, ring conformation (pyranoside and furanoside), composition, and overall glycan conformation. The software supports both X-ray crystallography and cryo-electron microscopy (cryo-EM) data. It interacts directly with refinement software to restrain sugar rings into their lowest-energy (most stable) conformations.
