Carbohydrate Structure Database: Difference between revisions

Revision as of 17:50, 21 August 2018

Revision as of 23:43, 15 October 2018

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The main data stored in CSDB are [[carbohydrate]] structures of bacterial, fungal, and plant origin. Each structure is assigned to an organism and is provided with the link(s) to the corresponding scientific publication(s), in which it was described. Apart from structural data, CSDB also stores [[Nuclear Magnetic Resonance Spectroscopy|NMR]] spectra, information on methods used to decipher a particular structure, and some other data.<ref name="Merged_CSDB" /><ref>{{cite journal| author=Harvey D.J.| date=2015|journal=Mass Spectrometry Reviews |title=Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012|doi=10.1002/mas.21471|PMID=26270629}}</ref>

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 chemicalChemical informationInformation and modelingModeling |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|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 chemicalChemical informationInformation and modelingModeling |volume=56|pages=1100–1104 |title=Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software|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=957-963957–963 |title=GRASS: semi-automated NMR-based structure elucidation of saccharides|doi = 10.1093/bioinformatics/btx696|PMID=29092007}}</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}}</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}}</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}}</ref>