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====Carbohydrates====
[[File:(A)-ASN297.svg|thumb|A 2D diagram of an N-glycan linked to an antibody fragment in the structure with PDB accession code '{{PDB2|4BYH}}'. This diagram, which has been generated with Privateer,<ref name=":0"/> follows the standard symbol nomenclature<ref name=":1"/> and includes, in its original svg format, annotations containing validation information, including ring conformation and detected monosaccharide types.]]
The branched and cyclic nature of carbohydrates poses particular problems to structure validation tools.<ref>{{cite journal | vauthors = Agirre J, Davies GJ, Wilson KS, Cowtan KD | title = Carbohydrate structure: the rocky road to automation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 39–47 | date = June 2017 | pmid = 27940408 | doi = 10.1016/j.sbi.2016.11.011 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf | series = Carbohydrates • Sequences and topology }}</ref> 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.<ref>{{cite journal | vauthors = Crispin M, Stuart DI, Jones EY | title = Building meaningful models of glycoproteins | journal = Nature Structural & Molecular Biology | volume = 14 | issue = 5 | pages = 354; discussion 354–5 | date = May 2007 | pmid = 17473875 | doi = 10.1038/nsmb0507-354a | s2cid = 2020697 | doi-access = free }}</ref> Also, monosaccharides have clear conformational preferences (saturated rings are typically found in chair conformations),<ref>{{cite journal | vauthors = Davies GJ, Planas A, Rovira C | title = Conformational analyses of the reaction coordinate of glycosidases | journal = Accounts of Chemical Research | volume = 45 | issue = 2 | pages = 308–16 | date = February 2012 | pmid = 21923088 | doi = 10.1021/ar2001765 }}</ref> but errors introduced during model building and/or refinement (wrong linkage chirality or distance, or wrong choice of model - see<ref>{{cite journal | vauthors = Agirre J | title = Strategies for carbohydrate model building, refinement and validation | journal = Acta Crystallographica Section D | volume = 73 | issue = Pt 2 | pages = 171–186 | date = February 2017 | pmid = 28177313 | pmc = 5297920 | doi = 10.1107/S2059798316016910 | url = http://journals.iucr.org/d/issues/2017/02/00/ba5257/ }}</ref> for recommendations on carbohydrate model building and refinement and<ref>{{cite journal | vauthors = Lütteke T | title = Analysis and validation of carbohydrate three-dimensional structures | journal = Acta Crystallographica Section D | volume = 65 | issue = Pt 2 | pages = 156–68 | date = February 2009 | pmid = 19171971 | pmc = 2631634 | doi = 10.1107/S0907444909001905 }}</ref><ref>{{cite book | vauthors = Lütteke T, von der Lieth CW | title = Glycomics | chapter = Data mining the PDB for glyco-related data | series = Methods in Molecular Biology | volume = 534 | pages = 293–310 | date = 2009-01-01 | pmid = 19277543 | doi = 10.1007/978-1-59745-022-5_21 | isbn = 978-1-58829-774-7 }}</ref><ref>{{cite journal | vauthors = Joosten RP, Lütteke T | title = Carbohydrate 3D structure validation | journal = Current Opinion in Structural Biology | volume = 44 | pages = 9–17 | date = June 2017 | pmid = 27816840 | doi = 10.1016/j.sbi.2016.10.010 | url = http://eprints.whiterose.ac.uk/109296/1/COStBi_postprint.pdf }}</ref> for reviews on general errors in carbohydrate structures) can bring their atomic models out of their energy minima. Around 20% of the deposited carbohydrate structures are in unjustified energy minima.<ref>{{cite journal | vauthors = Agirre J, Davies G, Wilson K, Cowtan K | title = Carbohydrate anomalies in the PDB | journal = Nature Chemical Biology | volume = 11 | issue = 5 | pages = 303 | date = May 2015 | pmid = 25885951 | doi = 10.1038/nchembio.1798 | url = http://eprints.whiterose.ac.uk/95242/1/AgirreDaviesWIlsonCowtan_self_archived.pdf | doi-access = free }}</ref>
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