Table 3.
Tools for structural validation of carbohydrates.
| Tool | Description | Type a | Reference |
|---|---|---|---|
| CNS | Macromolecular structure determination and refinement (including carbohydrates and glycoproteins) based on X-ray and NMR data | Standalone software | [327,328,329,330] (http://cns-online.org/v1.3/) |
| pdb-care | Identification and assigning carbohydrate structures using atom types and coordinates from PDB files | Web-tool | [326] (http://www.glycosciences.de/tools/pdb-care/) |
| CARP | Glycoprotein 3D quality evaluation based on the analysis of glycosidic torsion angles from PDB | Web-tool | [283] (http://www.glycosciences.de/tools/carp/) |
| GlyProbity | Accuracy and internal consistency check of carbohydrate 3D structures | Part of web-service pipeline | [257] (https://dev.glycam.org/portal/gf_home/) |
| PDB2Glycan | 3D structure analysis and validation of glycoprotein PDB entries | Part of web-service pipeline | [61] (https://glyconavi.org/TCarp/) (https://gitlab.com/glyconavi/pdb2glycan) |
| PDB-REDO | Glycoprotein structure model improvement and validation | Web-service; standalone software | [295,325] (https://pdb-redo.eu/) |
| Coot | Refinement and validation of glycoprotein 3D structure from cryoEM and X-ray crystallography data | Standalone software | [298,331] (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) |
| Rosetta Carbohydrate | Refinement of glycoprotein 3D structure from cryoEM and X-ray crystallography data, based on correction of conformational and configurational errors in carbohydrates | Python framework | [296] (https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans) |
| Privateer | Automated validation of carbohydrate conformation data based on 3D structure analysis | Standalone software | [297,332] (https://smb.slac.stanford.edu/facilities/software/ccp4/html/privateer.html) |
| Phenix | Determination, refinement and validation of macromolecular structure (including carbohydrates and glycoproteins) from cryoEM, X-ray diffraction and neutron diffraction crystallography data | Standalone software | [244] (http://phenix-online.org/) |
| Motive Validator | Automatic custom residue validation in biomolecules, including carbohydrates | Web-service | [333] (https://webchem.ncbr.muni.cz/Platform/MotiveValidator) |
| ValidatorDB | Pre-computed validation results of ligands and non-standard residues in PDB (including carbohydrates) | Web-service | [334] (http://webchem.ncbr.muni.cz/Platform/ValidatorDb) |
a See footnote a to Table 2.