Ten years of Integrative Carbohydrate Structure Validation with Privateer

Understanding glycoprotein structures is critical for understanding their biological roles, yet despite the moderate size of the glycans, determining the structure of these atomic models presents unique challenges. Originally designed to help mine the Protein Data Bank for monosaccharides and their context, the Privateer carbohydrate validation software has evolved to become ubiquitous in carbohydrate model building workflows. Privateer detects issues affecting sugar stereochemistry, regiochemistry, pyranoside and furanoside ring conformation, as well as overall glycan conformation and composition. Supporting both X-ray crystallography and cryo-electron microscopy data, Privateer can communicate with refinement software to help restrain sugar rings to their minimal-energy conformations. In this work, we reflect on a decade of Privateer, documenting its core processes and best practices to serve as the primary citation for the software.