. 2020 Oct 18;21(20):7702. doi: 10.3390/ijms21207702

Table 1.

Carbohydrate databases with 3D structure support.

Database	Years ^a	Description ^b	Data Coverage	Carbohydrate 3D Structures	References
Structure-centric
Carbohydrate Structure Database (CSDB)	2005– present	structures from prokaryotes, plants, and fungi taxonomy diseases bibliography curated	24669 structures 12521 organisms 9353 publications 2096 glycosyltransferase activities 13378 NMR spectra (¹H, ¹³C)	1327 disaccharide conformational maps 3D atomic coordinate generation	[28,42,43,44] (http://csdb.glycoscience.ru/database)
Glycosciences.DE	1997– present	taxonomy bibliography	26559 structures 20211 publications 3434 NMR spectra (¹H, ¹³C)	13599 3D structure models 12098 PDB entries (1880 distinct glycan structures) 2585 conformational maps 3D atomic coordinate generation	[45,46,47] (http://www.glycosciences.de/)
Glyco3D	2015– present	taxonomy bibliography curated	245 monosaccharides 125 disaccharides 314 bio-oligosaccharides 140 polysaccharides 415 GT structures 88 mAb structures 46 GAG structures 1662 lectin structures X-ray data * NMR data * molecular modeling data *	3035 3D structures * PDB entries * disaccharide conformational maps * 3D atomic coordinate generation	[48,49] (http://glyco3d.cermav.cnrs.fr/home.php)
PolySac3DB	2012– present	polysaccharides taxonomy bibliography curated	157 structures 84 publications X-ray data * NMR data * molecular modeling data *	157 3D structures PDB entries * conformational maps *	[50] (http://glyco3d.cermav.cnrs.fr/home.php)
EK3D	2016– present	E. coli K antigens bibliography curated	molecular modeling data protein data	72 3D structures 3D atomic coordinate generation	[51] (www.iith.ac.in/EK3D/)
3DSDSCAR	2010– present	sialic acid-containing oligosaccharides aqueous molecular dynamics simulations	27 structures	92 3D conformational models	[52,53] (http://aliffishbay.com/Domains/3dsdscar.org/3dsdscar.html)
MatrixDB	2011– present	protein–polysaccharide interactions taxonomy genetic data bibliography curated	58 GAG sequences proteoglycan structures * 1507 experiments 1058 experimentally supported associations 269 publications	3D structures * PDB entries * 3D-atomic coordinates generation (GAGs)	[54,55,56] (http://matrixdb.univ-lyon1.fr/)
EPS-DB	2017– present	bacterial exopolysaccharides functional properties genetic data taxonomy bibliography curated	105 structures	85 3D structure models 3D-atomic coordinates generation	[57] (http://www.epsdatabase.com)
GlyMDB	2020– present	glycan microarrays	5203 glycan microarray samples	1965 3D structures (PDB entries) 771 3D structures with glycan ligands (PDB entries)	[58] (http://www.glycanstructure.org/glymdb/)
CFG Glycan Structures Database	2006– present	mammalian glycan arrays taxonomy biological sources diseases bibliography	N-glycans * O-glycans *	3D-atomic coordinates generation	[59,60] (http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp) (http://www.functionalglycomics.org/glycomics/publicdata/selectedScreens.jsp)
Glycoproteomic
GlycoNAVI Tcarp	2020– present	diseases genetic data taxonomy bibliography	2723 unique analyzed glycans 5814 glycoproteins 712 lectins	3D structures * 15003 PDB entries 3D atomic coordinate generation	[61] (https://glyconavi.org/TCarp/)
GlyCosmos	2017– present	diseases genetic data taxonomy	109854 glycans glycolipids * 50113 glycoproteins 1238 lectins 20580 glycogenes	3D structures (PDB and UniProtKB entries) *	[13,62,63] (https://glycosmos.org/)
SugarBind	2010– present	adherence to pathogens taxonomy diseases bibliography curated	739 lectins 204 glycan ligands 567 pathogenic agents 1266 bindings 183 publications	3D lectin structures (PDB entries) *	[64] (https://sugarbind.expasy.org/)
GlyConnect	2019– present	protein glycosylation taxonomy biological sources diseases bibliography curated	2662 glycoproteins 3609 glycans 246 organisms 5675 sites 913 publications	3D glycoprotein structures (PDB entries) *	[65] (https://glyconnect.expasy.org/)
ProGlycProt	2012– present	prokaryotes taxonomy bibliography homology models * curated	crystal structures 61 glycoproteins 62 glycosyltransferases 38 enzymes/proteins involved in protein glycosylation 518 publications	3D structures (PDB entries) * 3D homology models (UniProtKB entries) *	[66,67] (http://www.proglycprot.org/)
ProCarbDB	2020– present	protein-carbohydrate complexes taxonomy bibliography binding affinities curated	5254 complexes 867 ligand monomers X-ray data	5254 3D structures (PDB entries)	[68] (http://www.procarbdb.science/procarb/)
Procaff	2019– present	protein-carbohydrate complexes taxonomy bibliography	3122 entries 228 publications 125 organisms 354 proteins 835 carbohydrates thermodynamic data	335 3D structures (PDB entries)	[69] (https://web.iitm.ac.in/bioinfo2/procaff/index.html)
GBSDB	2020– present	protein-carbohydrate complexes curated	6402 carbohydrate-containing PDB structures 12075 binding sites	6402 3D structures (PDB entries)	[70] (http://www.glycanstructure.org/gbs-db/pdb/)
PROCARB	2010– present	protein-carbohydrate complexes	604 complexes 48 modeled glycoproteins 100 unique carbohydrate ligands	604 complexes 3D structures (PDB entries) 26 N-linked 3D homology models 22 O-linked 3D homology models	[71] (http://www.procarb.org/procarbdb/)
UniLectin3D	2019– present	lectins taxonomy bibliography curated	2207 structures (1401 interacting with glycan) 535 distinct lectin sequences 228 distinct glycans 896 publications X-ray data	3D structures (PDB entries) *	[72,73] (https://www.unilectin.eu/unilectin3D/)
Lectin Frontier	2015– present	lectins taxonomy bibliography	398 structures binding affinities	3D structures (PDB entries) *	[74] (https://acgg.asia/lfdb2/)
LectinDB	2006– present	lectins taxonomy (all domains, incl. viruses) bibliography curated	789 organisms 821 PDB entries	PDB entries *	[75] (http://proline.physics.iisc.ernet.in/lectindb/)
GlycoEpitope	2006– present	epitopes taxonomy diseases functions receptors bibliography curated	178 epitopes 624 antibodies	PDB entries (epitopes) *	[76,77,78] (https://www.glycoepitope.jp/epitopes)
GlycoCD	2012– present	glycan CD antigens bibliography curated	19 glycan CDs 44 CRD-CDs	PDB entries *	[79] (http://www.glycosciences.de/glyco-cd/)
SACS	2002– present	antibodies automatically-updated	3994 entries crystal/EM structure data	PDB entries *	[80] (http://www.bioinf.org.uk/abs/sacs/xslt.cgi?src=antibodies.xml&xsl=summary.xsl)
SabDab	2014– present	antibodies automatically-updated taxonomy binding affinities curated	4223 entries 111 carbohydrate-containing antigen types experimental data	111 3D structures (PDB entries)	[81] (http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/)
CAZy	1998– present	carbohydrate-active enzymes and carbohydrate-binding modules taxonomy genetic data bibliography curated	CAZy structures * CAZy activities *	7500 ^c 3D structures bearing glycan-containing ligand or a glycan analog revealing enzyme-glycan interactions (PDB entries)	[82,83,84] (http://www.cazy.org/)
dbPTM	2006– present	protein post-translational modifications taxonomy diseases genetic data bibliography curated	32 C-linked glycosylations 3289 N-linked glycosylations 1860 O-linked glycosylations 6 S-linked glycosylations	3D structures (UniProtKB entries) *	[85,86,87] (http://dbptm.mbc.nctu.edu.tw/)
SWISS-MODEL Repository	2004– present	3D protein homology models taxonomy regularly updated	glycoprotein structures * 1698194 models from SWISS-MODEL for UniProtKB 158670 structures from PDB with mapping to UniProtKB	3D structures (PDB and UniProtKB entries) *	[88,89,90] (https://swissmodel.expasy.org/repository)
Specialized
GlycoMaps DB	2004– present	di- to pentasaccharides	in vacuo high-temperature molecular dynamics	conformational maps for 2585 glycosidic linkages	[91] (http://www.glycosciences.de/modeling/glycomapsdb/)
GFDB	2013– present	glycosidic torsion angles clustering analysis	1754 ^c unique glycan sequences in PDB 9055 ^c unique fragments with chemical modifications 127202 ^c fragment structures	PDB entries * 3D-atomic coordinates generation	[92] (http://www.glycanstructure.org/fragment-db)
GLYCAM-Web	2013– present	mammalian glycans	pre-built libraries of predicted 3D structures of common bioglycans	3D structure models * 3D-atomic coordinates generation	(http://glycam.org/Pre-builtLibraries.jsp)

^a Where unknown, the year of the first publication is given. ^b Database is marked as curated if manual verification of data was reported in the original publication or at the database web site. ^c Published coverage data can be outdated; database interface provides no statistics on current coverage. * Database provides no search facilities for indicated carbohydrate 3D structural data.