The branched and cyclic nature of carbohydrates poses particular problems to structure validation tools. At higher resolutions, it is possible to determine the sequence/structure of oligo- and poly-saccharides, both as covalent modifications and as ligands. However, at lower resolutions (typically lower than 2.0Å), sequences/structures should either match known structures, or be supported by complementary techniques such as Mass Spectrometry. Also, monosaccharides have clear conformational preferences (saturated rings are typically found in chair conformations), but errors introduced during model building and/or refinement (wrong linkage chirality or distance, or wrong choice of model - see for recommendations on carbohydrate model building and refinement and for reviews on general errors in carbohydrate structures) can bring their atomic models out of the more likely low-energy state. Around 20% of the deposited carbohydrate structures are in a higher-energy conformation not justified by the structural data (measured using real-space correlation coefficient).
A number of carbohydrate validation web services are available at [http://ww.glycosciences.de glycosciences.de] (including nomenclature checks and linkage checks by [http://www.glycosciences.de/tools/pdb-care/ pdb-care], and cross-validation with Mass Spectrometry data through the use of GlycanBuilder), whereas the CCP4 suite currently distributes [http://www.ccp4.ac.uk/html/privateer.html Privateer], which is a tool that is integrated into the model building and refinement process itself. Privateer is able to check stereo- and regio-chemistry, ring conformation and puckering, linkage torsions, and real-space correlation against positive omit density, generating aperiodic torsion restraints on ring bonds, which can be used by any refinement software in order to maintain the monosaccharide's minimal energy conformation.
Privateer also generates scalable two-dimensional SVG diagrams according to the Essentials of Glycobiology standard symbol nomenclature containing all the validation information as tooltip annotations (see figure). This functionality is currently integrated into other CCP4 programs, such as the molecular graphics program CCP4mg (through the Glycoblocks 3D representation, which conforms to the standard symbol nomenclature) and the suite's graphical interface, CCP4i2.