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Created on: 09-Sep-2012   Last updated on: 10-May-2013 |  How to cite this?
Total resources - 27
A compilation of carbohydrate resources
Sravanthi Davuluri, Akhilesh Bajpai and Vishalavani Nidagundi (Correspondence: Acharya KK, kshitish@ibab.ac.in)
 Click here for additional comparative study/note

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
geoRge
https://github.com/jcapelladesto/geoRge.
A Computational Tool To Detect the Presence of Stable Isotope Labeling in LC/MS-Based Untargeted Metabolomics
Capellades J, Navarro M, Samino , Garcia-Ramirez M, Hernandez C, Simo R, Vinaixa M, Yanes O;geoRge: A Computational Tool To Detect the Presence of Stable Isotope Labeling in LC/MS-Based Untargeted Metabolomics.Anal Chem. 2016 Jan 5;88(1):621-8. doi: 10.1021/acs.analchem.5b03628. Epub 2015 Dec 18.PMID: 26639619
2016
1
CAZy
http://www.cazy.org
Provides details about the Carbohydrate-Active enZYmes.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8. doi: 10.1093/nar/gkn663. Epub 2008 Oct 5. PubMed PMID: 18838391; PubMed Central PMCID: PMC2686590.
2008
32
CFG Functional Glycomics gateway
http://www.functionalglycomics.org
Provides access to primary experimental data like that from glycan microarray screen.
Not available
Not available
84
GBP - Glycan Binding Proteins
http://www.functionalglycomics.org/glycomics/molecule/jsp/gbpMolecule-home.jsp
Provides the information about the glycan binding proteins.
Not available
Not available
94
CSDB
http://csdb.glycoscience.ru.
Carbohydrate Structure Database.
K.S. Egorova, A.N. Kondakova, and Ph.V. Toukach; Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes; Database (Oxford). 2015 Sep 3; doi: 10.1093/database/bav073 ;PMID: 26337239 PMCID: PMC4559136..
2015
94
BCSDB - Bacterial carbohydrate structure database
http://csdb.glycoscience.ru/bacterial
Provides detailed carbohydrate structural information that is derived from many bacterial species.
Toukach PV. Bacterial carbohydrate structure database 3: principles andrealization. J Chem Inf Model. 2011 Jan 24;51(1):159-70. doi: 10.1021/ci100150d. Epub 2010 Dec 14. PubMed PMID: 21155523.
2011
96
dbCAN - Carbohydrate-active enzymes
http://csbl.bmb.uga.edu/dbCAN/annotate.php
Provides signature domain annotation information for CAZyme (carbohydrate-active enzyme) families.
Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. dbCAN: a web resource for automatedcarbohydrate-active enzyme annotation. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51. doi: 10.1093/nar/gks479. Epub 2012 May 29. PubMed PMID: 22645317;PubMed Central PMCID: PMC3394287.
2012
98
GLYCO3D
http://glyco3d.cermav.cnrs.fr/
Provides the integration of few databases (BiOligo, Lectin3D, GAG, mAbs, GT, Polysac3DB) and relevant information.
Not available
Not available
98
GLYCOSCIENCES.de
http://www.glycosciences.de/.
Provides details about glycobiology and glycomics.
Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth CW.GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiologyresearch. Glycobiology. 2006 May;16(5):71R-81R. Epub 2005 Oct 20. Review. PubMed PMID: 16239495.
2006
98
MatrixDB
http://matrixdb.ibcp.fr/
Provides information about protein-protein and protein-carbohydrate interactions.
Chautard E, Ballut L, Thierry-Mieg N, Ricard-Blum S. MatrixDB, a databasefocused on extracellular protein-protein and protein-carbohydrate interactions.Bioinformatics. 2009 Mar 1;25(5):690-1. doi: 10.1093/bioinformatics/btp025. Epub 2009 Jan 15. PubMed PMID: 19147664; PubMed Central PMCID: PMC2647840.
2009
98
UniCarbKB
http://www.unicarbkb.org/
This database provides information about mammalian glycobiology.
Matthew P. Campbell, , Nicolle H. Packer; UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations.Biochim Biophys Acta. 2016 Aug;1860(8):1669-75. doi: 10.1016/j.bbagen.2016.02.016. Epub 2016 Mar 3;PMID: 26940363
2016
99
3D Lectine Database
http://lectin3d.cermav.cnrs.fr
Provides information about lectins from different species.
Not available
Not available
100
3DSDSCAR - Three dimensional structural database for sialic acid-containing carbohydrates
http://www.3dsdscar.org./
Provides information about 3D structural database for sialic acid-containing carbohydrates (3DSDSCAR).
Veluraja K, Selvin JF, Venkateshwari S, Priyadarzini TR. 3DSDSCAR--a threedimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation. Carbohydr Res. 2010 Sep 23;345(14):2030-7. doi:10.1016/j.carres.2010.06.021. Epub 2010 Jul 8. PubMed PMID: 20691432.
2010
100
BPGD
http://sydney.edu.au/science/molecular_bioscience/BPGD
Database describes about bacterial polysaccharide genes.
Not available
Not available
100
EuroCarbDB
http://www.ebi.ac.uk/eurocarb/home.action
Database with structures of carbohydrates and experimental data. It provides details about unique taxonomies, tissues, diseases, perturbations and 0-glycoconjugates.
von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, DellA, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K,Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T,Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, SchloissnigS, Stenutz R, Vranken WF, Widmalm G, Haslam SM. EUROCarbDB: An open-accessplatform for glycoinformatics. Glycobiology. 2011 Apr;21(4):493-502. doi:10.1093/glycob/cwq188. Epub 2010 Nov 23. PubMed PMID: 21106561; PubMed CentralPMCID: PMC3055595.
2010
100
GlycomeDB
http://www.glycome-db.org/
Provides the structural information for 11,822 carbohydrates.
Ranzinger R, Herget S, von der Lieth CW, Frank M. GlycomeDB - a unifieddatabase for carbohydrate structures. Nucleic Acids Res. 2011 Jan;39(Databaseissue):D373-6. doi: 10.1093/nar/gkq1014. Epub 2010 Nov 2. PubMed PMID: 21045056; PubMed Central PMCID: PMC3013643.
2010
100
KEGG GLYCAN
http://www.genome.jp/kegg/glycan
Database provides the information about molecular interaction networks as well as glycan biosynthesis and metabolism.
Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, KawasakiT, Kanehisa M. KEGG as a glycome informatics resource. Glycobiology. 2006May;16(5):63R-70R. Epub 2005 Jul 13. Review. PubMed PMID: 16014746.
2006
100
Mucin Database
http://www.medkem.gu.se/mucinbiology/databases
Provides details about mucin genes, transcripts, protein sequences and functional domains.
Lang T, Hansson GC, Samuelsson T. Gel-forming mucins appeared early inmetazoan evolution. Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16209-14. Epub2007 Oct 2. PubMed PMID: 17911254; PubMed Central PMCID: PMC2042186.
2007
100
O-GlycBase
http://www.cbs.dtu.dk/databases/OGLYCBASE
Provides details about glycoproteins as well as O-linked glycosylation sites.
Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE. O-GLYCBASE version 4.0: arevised database of O-glycosylated proteins. Nucleic Acids Res. 1999 Jan1;27(1):370-2. PubMed PMID: 9847232; PubMed Central PMCID: PMC148187.
1999
100
PROCARB
http://www.procarb.org
Provides information about protein-carbohydrate complexes.
Malik A, Firoz A, Jha V, Ahmad S. PROCARB: A Database of Known and ModelledCarbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools. AdvBioinformatics. 2010:436036. doi: 10.1155/2010/436036. Epub 2010 Jun 29. PubMedPMID: 20671979; PubMed Central PMCID: PMC2909730.
2010
100
CSDB_GT
http://csdb.glycoscience.ru/gt.html.
Carbohydrate Structure Glycosyltransferase Database is a new database that provides 780 activities that are exhibited by Glycosyltransferases as well as several others that are found in Arabidopsis thaliana. It is linked to o the Carbohydrate Structure Database (CSDB)
Ksenia S Egorova Philip V Toukach.CSDB_GT: a new curated database on glycosyltransferases. Glycobiology (2017) 27 (4): 285-290;03 January 2017; https://doi.org/10.1093/glycob/cww137; PMID: 28011601
2017
100
FOODPRO
it is a web based tool that inlcudes a food NMR spectrum database and evaluates covariance and correlation spectra to tasting and hardness[ roughly catagorized into fish and vegetable group
Chikayama E, Yamashina R, Komatsu K, Tsuboi Y, Sakata K, Kikuchi J, Sekiyama Y..FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes. Metabolites. 2016 Oct 19;6(4). pii: E36. DOI: 10.3390/metabo6040036; PMID: 27775560 PMCID: PMC5192442
2016
100
CarbBuilder
https://people.cs.uct.ac.za/~mkuttel/Downloads.html
CarbBuilder is a portable software tool capable of producing 3D molecular models of carbohydrates from the simple text specification of a primary structure. It can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Freely available
Michelle M. Kuttel, Jonas Stĺhle,Göran Widmalm.CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures.J Comput Chem. 2016 Aug 15;37(22):2098-105. doi: 10.1002/jcc.24428. Epub 2016 Jun 18. PMID: 27317625
2016
100
 UniCorn
https://github.com/haifengl/unicorn
A theoretical N-glycan structure database. Provides information about experimentally described glycan structures
Akune Y, Lin CH, Abrahams JL, Zhang J, Packer NH, Aoki-Kinoshita KF, Campbell MP.Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.Carbohydr Res. 2016 Aug 5;431:56-63. doi: 10.1016/j.carres.2016.05.012. Epub 2016 May 30;PMID: 27318307
2016
100
PlantCAZyme
http://cys.bios.niu.edu/plantcazyme/
A database of carbohydrate active enzymes (CAZymes) for plant carbohydrates
Alexander Ekstrom, Rahil Taujale, Nathan McGinn1 and Yanbin Yin.PlantCAZyme: a database for plant carbohydrate-active enzymes,Database (Oxford). 2014 Aug 14,1–8,DOI: 10.1093/database/bau079,PMID: 25125445 PMCID: PMC4132414
2014
100
Privateer
http://www.ccp4.ac.uk/html/privateer.html
It is a software package aimed at the conformational validation of carbohydrate structures
Jon Agirre, Javier Iglesias-Fernández, Carme Rovira, Gideon J Davies, Keith S Wilson & Kevin D Cowtan.Privateer: software for the conformational validation of carbohydrate structures;Nature Structural & Molecular Biology 22, 833–834,2015 November 04 doi:10.1038/nsmb.3115.PMID: 26581513
2015
100
GlycoCD
http://glycosciences.de/glycocd/index.php
This database provides information about carbohydrate moieties and proteins interactions.
Sonu Kumar Thomas Lütteke Reinhard Schwartz-Albiez;GlycoCD: a repository for carbohydrate-related CD antigens; Bioinformatics. 2012 Oct 1;28(19):2553-5. Epub 2012 Jul 30, PMID: 22847935
2012
100
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