Carbohydrate Structure Database: Difference between revisions

Revision as of 12:08, 8 March 2020

Revision as of 04:52, 12 April 2020

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CSDB provides access to several carbohydrate-related research tools:

* Simulation of 1D and 2D [[NMR]] spectra of [[carbohydrates]] ([http://csdb.glycoscience.ru/database/index.html?help=nmr GODESS: glycan-oriented dual empirical spectrum simulation]).<ref name="GODESS">{{cite journal| author=Kapaev R.R.| author2=Egorova K.S.| author3=Toukach Ph.V.|date=2014|journal=Journal of Chemical Information and Modeling |volume=54|issue=9|pages=2594–2611 |title=Carbohydrate structure generalization scheme for database-driven simulation of experimental observables, such as NMR chemical shifts|doi = 10.1021/ci500267u|pmid=25020143}}</ref><ref name="GODESS_1H">{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2015|journal=Analytical Chemistry |volume=87|pages=7006–7010 |title=Improved carbohydrate structure generalization scheme for ¹H and ¹³C NMR simulations| issue=14|doi=10.1021/acs.analchem.5b01413|pmid=26087011}}</ref><ref name="GODESS_2D">{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2016|journal=Journal of Chemical Information and Modeling |volume=56|pages=1100–1104 |title=Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software| issue=6|doi=10.1021/acs.jcim.6b00083|pmid=27227420}}</ref>

* Automated [[NMR]]-based structure elucidation ([http://csdb.glycoscience.ru/database/index.html?help=nmr#grass GRASS: generation, ranking and assignment of saccharide structures]).<ref name="GRASS">{{cite journal| author=Kapaev R.R.| author2=Toukach Ph.V.|date=2018|journal=Bioinformatics |volume=34|issue=6|pages=957–963 |title=GRASS: semi-automated NMR-based structure elucidation of saccharides|doi = 10.1093/bioinformatics/btx696|pmid=29092007|doi-access=free}}</ref>

* [[Statistical analysis]] of structural feature distribution in [[glycomes]] of living organisms<ref name="taxon_clustering">{{cite journal| author=Egorova K.S.|author2=Kondakova A.N.|author3=Toukach Ph.V.| date=2015|journal=Database |pages=ID bav073 |title=Carbohydrate structure database: tools for statistical analysis of bacterial, plant and fungal glycomes|doi=10.1093/database/bav073|pmid=26337239|pmc=4559136|volume=2015}}</ref><ref name="Statistics">{{cite journal| author=Herget S.| author2=Toukach Ph.V.| author3=Ranzinger R.| author4=Hull W.E.| author5=Knirel Y.| author6=von der Lieth C.-W.| date=2008|journal=BMC Structural Biology |volume=8|pages=ID 35 |title=Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans|doi=10.1186/1472-6807-8-35|pmid=18694500| pmc=2543016}}</ref>

* Generation of optimized atomic coordinates for an arbitrary [[saccharide]]<ref name="RESTLESS">{{cite journal| author=Chernyshov I.Y.| author2=Toukach Ph.V.|date=2018|journal=Bioinformatics |title=REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates|doi = 10.1093/bioinformatics/bty168|pmid=29547883|volume=34| issue=15|pages=2679–2681|doi-access=free}}</ref>

* [[Taxon]] [[Cluster analysis|clustering]] based on similarities of [[glycomes]] (carbohydrate-based [[Tree of life (biology)|tree of life]])<ref name="taxon_clustering" />

* [[Glycosyltransferase]] subdatabase ([http://csdb.glycoscience.ru/gt.html GT-explorer])<ref name="CSDB_GT">{{cite journal| author= Toukach Ph.V.| author2=Egorova K.S. |date=2016|journal=Glycobiology |volume=in production|title=CSDB_GT: a new curated database on glycosyltransferases| issue=4 | pages=285–290 |doi=10.1093/glycob/cww137| pmid=28011601 |doi-access=free}}</ref>

==History and funding==

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The data are selected and added to CSDB manually by browsing original scientific publications. The data originating from other databases are subject to error-correction and approval procedures.<ref name="Critical">{{cite journal| author=Egorova K.S.| author2=Toukach Ph.V.| date=2012|journal=Journal of Chemical Information and Modeling |volume=52|pages=2812–2814 |title=Critical analysis of CCSD data quality| issue=11|doi=10.1021/ci3002815|pmid=23025661}}</ref>

As of the beginning of 2017, the coverage on [[bacteria]] and [[archaea]] is ca. 80% of carbohydrate structures published in scientific literature in the years 1943 - 2015.<ref name="Merged_CSDB"/> The time lag between the publication of relative data and their deposition into CSDB is about 18 months. Plants are covered up to 1997, and fungi up to 2005.<ref name="PFCSDB">{{cite journal| author=Egorova K.S.| author2=Toukach Ph.V.| date=2013|journal=Carbohydrate Research |volume=389|pages=112–114|title=Expansion of coverage of Carbohydrate Structure Database (CSDB)|doi=10.1016/j.carres.2013.10.009|pmid=24680503}}</ref>

CSDB does not cover data from the [[animalia]] ___domain, except [[Protozoa|unicellular metazoa]]. There is a number of dedicated databases on [[animal]] [[carbohydrates]], e.g. [http://www.unicarbkb.org/ UniCarbKB] <ref name="unicarbkb">{{cite journal|author=Campbell M.P.|author2=Packer N.H. | date=2016|journal=Biochimica et Biophysica Acta |volume=1860|issue=8 |pages=1669–1675 |title=UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations|doi=10.1016/j.bbagen.2016.02.016|pmid=26940363}}</ref> or [http://glycosciences.de GLYCOSCIENCES.de].<ref>{{cite journal|author=Lütteke T.|author2=Bohne-Lang A.|author3=Loss A.|author4=Goetz T.|author5=Frank M.|author6=von der Lieth C.-W.| date=2006|journal=Glycobiology|volume=16|issue=5 |pages=71R–81R |title=GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research|doi=10.1093/glycob/cwj049|pmid=16239495|doi-access=free}}</ref>

CSDB is reported as one of the biggest projects in [[glycoinformatics]].<ref>{{cite journal|author=Rigden D.J.|author2=Fernández-Suárez X.M.|author3=Galperin M.Y. | date=2016|journal=Nucleic Acids Research |volume=44|issue=D1 |pages=D1–D6 |title=The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection|doi=10.1093/nar/gkv1356|pmid=26740669 |pmc=4702933}}</ref><ref>{{cite journal|author=Aoki-Kinoshita K.F. | date=2013|journal=Molecular & Cellular Proteomics |volume=12|issue=4 |pages=1036–1045 |title=Using databases and web resources for glycomics research|doi=10.1074/mcp.R112.026252|pmid=23325765|pmc=3617328}}</ref><ref>{{cite journal|author=Frank M.|author2=Schloissnig S. | date=2010|journal=Cellular and Molecular Life Sciences |volume=67|issue=16 |pages=2749–2772 |title=Bioinformatics and molecular modeling in glycobiology.|doi=10.1007/s00018-010-0352-4|pmid=20364395 |pmc=2912727}}</ref><ref>{{cite journal|author=Artemenko N.V.|author2=McDonald A.G.|author3=Davey G.P.|author4=Rudd P.M. | date=2012|journal=Methods in Molecular Biology |volume=899 |pages=325–350 |title=Databases and tools in glycobiology|doi=10.1007/978-1-61779-921-1_21|pmid=22735963|isbn=978-1-61779-920-4}}</ref><ref>{{cite journal|author=Lütteke T. | date=2012|journal=Beilstein Journal of Organic Chemistry |volume=8 |pages=915–929 |title=The use of glycoinformatics in glycochemistry|doi=10.3762/bjoc.8.104|pmid=23015842 |pmc=3388882}}</ref><ref>{{cite journal|author=Zhulin I.B. | date=2015|journal=Journal of Bacteriology |volume=197|issue=15 |pages=2458–2467 |title=Databases for Microbiologists|doi=10.1128/JB.00330-15|pmid=26013493|pmc=4505447}}</ref><ref>{{cite journal|author=Yamada K.|author2=Kakehi K. | date=2011|journal=Journal of Pharmaceutical and Biomedical Analysis |volume=55|issue=4 |pages=702–727 |title=Recent advances in the analysis of carbohydrates for biomedical use|doi=10.1016/j.jpba.2011.02.003|pmid=21382683}}</ref> It is employed in structural studies of natural carbohydrates<ref>{{cite journal| author=Fontana C.|author2=Zaccheus M.|author3=Weintraub A.|author4=Ansaruzzaman M.|author5=Widmalm G.| date=2016|journal=Carbohydrate Research |volume=432 |pages=41–49 |title=Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-16000|doi=10.1016/j.carres.2016.06.004|pmid=27392309|url=http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-133271}}</ref><ref>{{cite journal| author=Potekhina N.V.|author2=Shashkov A.S.|author3=Senchenkova S.N.|author4=Dorofeeva L.V.|author5=Evtushenko L.I.| date=2012|journal=Biochemistry (Moscow) |volume=77 |issue=11 |pages=1294–1302 |title=Structure of hexasaccharide 1-phosphate polymer from Arthrobacter uratoxydans VKM Ac-1979(T) cell wall|doi=10.1134/S0006297912110089|pmid=23240567}}</ref><ref>{{cite journal| author=Chapot-Chartier M.P.|author2=Vinogradov E.|author3=Sadovskaya I.|author4=Andre G.|author5=Mistou M.Y.|author6=Trieu-Cuot P.|author7=Furlan S.|author8=Bidnenko E.|author9=Courtin P.|author10=Péchoux C.|author11=Hols P.|author12=Dufrêne Y.F.|author13=Kulakauskas S.| date=2010|journal=Journal of Biological Chemistry |volume=285|issue=14 |pages=10464–10471 |title=Cell surface of Lactococcus lactis is covered by a protective polysaccharide pellicle|doi=10.1074/jbc.M109.082958|pmid=20106971|pmc=2856253}}</ref> and in glyco-profiling.<ref>{{cite journal| author=Walsh I.|author2=Zhao S.|author3=Campbell M.|author4=Taron C.H.|author5=Rudd P.M.| date=2016|journal=Current Opinion in Structural Biology |volume=40 |pages=70–80 |title=Quantitative profiling of glycans and glycopeptides: an informatics' perspective|doi=10.1016/j.sbi.2016.07.022|pmid=27522273}}</ref>

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== Interrelation with other databases ==

CSDB is cross-linked to other [[glycomics]] databases,<ref>{{cite journal| author=Ranzinger R.|author2=Herget S.|author3=Wetter T.|author4=von der Lieth C.-W.| date=2008|journal=BMC Bioinformatics |volume=9 |pages=ID 384 |title=GlycomeDB - integration of open-access carbohydrate structure databases|doi=10.1186/1471-2105-9-384|pmid=18803830 |pmc=2567997}}</ref><ref name="Integration_1">{{cite journal| author=Toukach Ph.V.|author2=Joshi H.| author3=Ranzinger R.| author4=Knirel Y.| author5=von der Lieth C.-W.| date=2007|journal=Nucleic Acids Research - Database Issue |volume=35|pages=D280–D286|title=Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de|issue=Database issue|doi=10.1093/nar/gkl883|pmid=17202164| pmc=1899093}}</ref> such as [http://www.monosaccharidedb.org MonosaccharideDB], [http://glycosciences.de Glycosciences.DE], [https://www.ncbi.nlm.nih.gov/pubmed/ NCBI Pubmed], [https://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy], [https://www.ncbi.nlm.nih.gov/nlmcatalog NLM catalog], etc. Structures are presented in multiple carbohydrate notations (SNFG,<ref>{{cite journal|author=Varki A.|display-authors=et al | date=2015|journal=Glycobiology |volume=25|issue=12 |pages=1323–1324 |title=Symbol Nomenclature for Graphical Representations of Glycans|doi=10.1093/glycob/cwv091|pmid=26543186|pmc=4643639}}</ref> SweetDB,<ref>{{cite journal|author=Loss A.|author2=Bunsmann P.|author3=Bohne A.|author4=Loss A.|author5=Schwarzer E.|author6=Lang E.|author7=von der Lieth C.-W. | date=2002|journal=Nucleic Acids Research |volume=30|issue=1 |pages=405–408 |title=SWEET-DB: an attempt to create annotated data collections for carbohydrates|pmid=11752350 |doi=10.1093/nar/30.1.405 |pmc=99123}}</ref> GlycoCT,<ref>{{cite journal|author=Herget S.|author2=Ranzinger R.|author3=Maass K.|author4=von der Lieth C.-W.| date=2008|journal=Carbohydrate Research |volume=343|issue=12 |pages= 2162–2171|title=GlycoCT - a unifying sequence format for carbohydrates|doi=10.1016/j.carres.2008.03.011|pmid=18436199}}</ref> [http://www.wurcs-wg.org WURCS],<ref>{{cite journal|author=Tanaka K.|author2=Aoki-Kinoshita K.F.|author3=Kotera M.|author4=Sawaki H.|author5=Tsuchiya S.|author6=Fujita N.|author7=Shikanai T.|author8=Kato M.|author9=Kawano S.|author10=Yamada I.|author11=Narimatsu H. | date=2014|journal=Journal of Chemical Information and Modeling |volume=54|issue=6 |pages=1558–1566 |title=WURCS: the Web3 unique representation of carbohydrate structures|doi=10.1021/ci400571e|pmid=24897372|doi-access=free}}</ref> [http://glycam.org GLYCAM],<ref>{{cite journal|author=Kirschner K.N.|author2=Yongye A.B.|author3=Tschampel S.M.|author4=González-Outeiriño J.|author5=Daniels C.R.|author6=Foley B.L.|author7=Woods R.J. | date=2008|journal=Journal of Computational Chemistry |volume=29|issue=4 |pages=622–655 |title=GLYCAM06: a generalizable biomolecular force field. Carbohydrates|doi=10.1002/jcc.20820|pmid=17849372|pmc=4423547}}</ref> etc.). CSDB is exportable as a [[Resource Description Framework]] (RDF) feed according to the [https://bioportal.bioontology.org/ontologies/GLYCORDF GlycoRDF] ontology.<ref name="Ontology">{{cite journal| author=Ranzinger R.| author2=Aoki-Kinoshita K.F.| author3=Campbell M.P.| author4=Kawano S.| author5=Lütteke T.| author6=Okuda S.| author7=Shinmachi D.| author8=Shikanai T.| author9=Sawaki H.| author10=Toukach Ph.V.| author11=Matsubara M.| author12=Yamada I.| author13=Narimatsu H.|date=2015|journal=Bioinformatics|volume=31|issue=6|pages=919–925|title=GlycoRDF: An ontology to standardize Glycomics data in RDF|doi=10.1093/bioinformatics/btu732|pmid=25388145| pmc=4380026}}</ref><ref name="Integration_2">{{cite journal| author=Aoki-Kinoshita K.F.| author2=Bolleman J.| author3=Campbell M.P.| author4=Kawano S.| author5=Kim J.| author6=Lütteke T.| author7=Matsubara M.| author8=Okuda S.| author9=Ranzinger R.| author10=Sawaki H.| author11=Shikanai T.| author12=Shinmachi D.| author13=Suzuki Y.| author14=Toukach Ph.V.| author15=Yamada I.| author16=Packer N.H.| author17=Narimatsu H.| date=2013|journal=Journal of Biomedical Semantics |volume=4|pages=ID 39 |title=Introducing glycomics data into the Semantic Web| issue=1|doi=10.1186/2041-1480-4-39|pmid=24280648| pmc=4177142}}</ref>

==External links==