References analysis of the Wikipedia article "Carbohydrate Structure Database" in the English version

doi.org

Toukach Ph.V.; Egorova K.S. (2016). "Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts". Nucleic Acids Research. 44 (D1): D1229 – D1236. doi:10.1093/nar/gkv840. PMC 4702937. PMID 26286194.

Harvey D.J. (2015). "Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012". Mass Spectrometry Reviews. 36 (3): 255–422. doi:10.1002/mas.21471. PMID 26270629.

Kapaev R.R.; Egorova K.S.; Toukach Ph.V. (2014). "Carbohydrate structure generalization scheme for database-driven simulation of experimental observables, such as NMR chemical shifts". Journal of Chemical Information and Modeling. 54 (9): 2594–2611. doi:10.1021/ci500267u. PMID 25020143.

Kapaev R.R.; Toukach Ph.V. (2015). "Improved carbohydrate structure generalization scheme for ¹H and ¹³C NMR simulations". Analytical Chemistry. 87 (14): 7006–7010. doi:10.1021/acs.analchem.5b01413. PMID 26087011.

Kapaev R.R.; Toukach Ph.V. (2016). "Simulation of 2D NMR Spectra of Carbohydrates Using GODDESS Software". Journal of Chemical Information and Modeling. 56 (6): 1100–1104. doi:10.1021/acs.jcim.6b00083. PMID 27227420.

Kapaev R.R.; Toukach Ph.V. (2018). "GRASS: semi-automated NMR-based structure elucidation of saccharides". Bioinformatics. 34 (6): 957–963. doi:10.1093/bioinformatics/btx696. PMID 29092007.

Egorova K.S.; Kondakova A.N.; Toukach Ph.V. (2015). "Carbohydrate structure database: tools for statistical analysis of bacterial, plant and fungal glycomes". Database. 2015: ID bav073. doi:10.1093/database/bav073. PMC 4559136. PMID 26337239.

Herget S.; Toukach Ph.V.; Ranzinger R.; Hull W.E.; Knirel Y.; von der Lieth C.-W. (2008). "Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans". BMC Structural Biology. 8: ID 35. doi:10.1186/1472-6807-8-35. PMC 2543016. PMID 18694500.

Chernyshov I.Y.; Toukach Ph.V. (2018). "REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates". Bioinformatics. 34 (15): 2679–2681. doi:10.1093/bioinformatics/bty168. PMID 29547883.

Toukach Ph.V.; Egorova K.S. (2017). "CSDB_GT: a new curated database on glycosyltransferases". Glycobiology. 27 (4): 285–290. doi:10.1093/glycob/cww137. PMID 28011601.

Egorova K.S.; Knirel Y.A.; Toukach Ph.V. (2019). "Expanding CSDB_GT glycosyltransferase database with Escherichia coli". Glycobiology. 29 (4): 285–287. doi:10.1093/glycob/cwz006. PMID 30759212.

Doubet S.; Albersheim P. (1992). "CarbBank". Glycobiology. 2 (6): 505–507. doi:10.1093/glycob/2.6.505. PMID 1472756.

Egorova K.S.; Toukach Ph.V. (2012). "Critical analysis of CCSD data quality". Journal of Chemical Information and Modeling. 52 (11): 2812–2814. doi:10.1021/ci3002815. PMID 23025661.

Egorova K.S.; Toukach Ph.V. (2013). "Expansion of coverage of Carbohydrate Structure Database (CSDB)". Carbohydrate Research. 389: 112–114. doi:10.1016/j.carres.2013.10.009. PMID 24680503.

Campbell M.P.; Packer N.H. (2016). "UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations". Biochimica et Biophysica Acta (BBA) - General Subjects. 1860 (8): 1669–1675. doi:10.1016/j.bbagen.2016.02.016. PMID 26940363.

Lütteke T.; Bohne-Lang A.; Loss A.; Goetz T.; Frank M.; von der Lieth C.-W. (2006). "GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research". Glycobiology. 16 (5): 71R – 81R. doi:10.1093/glycob/cwj049. PMID 16239495.

Rigden D.J.; Fernández-Suárez X.M.; Galperin M.Y. (2016). "The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection". Nucleic Acids Research. 44 (D1): D1 – D6. doi:10.1093/nar/gkv1356. PMC 4702933. PMID 26740669.

Aoki-Kinoshita K.F. (2013). "Using databases and web resources for glycomics research". Molecular & Cellular Proteomics. 12 (4): 1036–1045. doi:10.1074/mcp.R112.026252. PMC 3617328. PMID 23325765.

Frank M.; Schloissnig S. (2010). "Bioinformatics and molecular modeling in glycobiology". Cellular and Molecular Life Sciences. 67 (16): 2749–2772. doi:10.1007/s00018-010-0352-4. PMC 2912727. PMID 20364395.

Artemenko N.V.; McDonald A.G.; Davey G.P.; Rudd P.M. (2012). "Databases and Tools in Glycobiology". Therapeutic Proteins. Methods in Molecular Biology. Vol. 899. pp. 325–350. doi:10.1007/978-1-61779-921-1_21. ISBN 978-1-61779-920-4. PMID 22735963.

Lütteke T. (2012). "The use of glycoinformatics in glycochemistry". Beilstein Journal of Organic Chemistry. 8: 915–929. doi:10.3762/bjoc.8.104. PMC 3388882. PMID 23015842.

Zhulin I.B. (2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15): 2458–2467. doi:10.1128/JB.00330-15. PMC 4505447. PMID 26013493.

Yamada K.; Kakehi K. (2011). "Recent advances in the analysis of carbohydrates for biomedical use". Journal of Pharmaceutical and Biomedical Analysis. 55 (4): 702–727. doi:10.1016/j.jpba.2011.02.003. PMID 21382683.

Fontana C.; Zaccheus M.; Weintraub A.; Ansaruzzaman M.; Widmalm G. (2016). "Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-16000". Carbohydrate Research. 432: 41–49. doi:10.1016/j.carres.2016.06.004. PMID 27392309. S2CID 23129802.

Potekhina N.V.; Shashkov A.S.; Senchenkova S.N.; Dorofeeva L.V.; Evtushenko L.I. (2012). "Structure of hexasaccharide 1-phosphate polymer from Arthrobacter uratoxydans VKM Ac-1979(T) cell wall". Biochemistry (Moscow). 77 (11): 1294–1302. doi:10.1134/S0006297912110089. PMID 23240567. S2CID 9699031.

Chapot-Chartier M.P.; Vinogradov E.; Sadovskaya I.; Andre G.; Mistou M.Y.; Trieu-Cuot P.; Furlan S.; Bidnenko E.; Courtin P.; Péchoux C.; Hols P.; Dufrêne Y.F.; Kulakauskas S. (2010). "Cell surface of Lactococcus lactis is covered by a protective polysaccharide pellicle". Journal of Biological Chemistry. 285 (14): 10464–10471. doi:10.1074/jbc.M109.082958. PMC 2856253. PMID 20106971.

Walsh I.; Zhao S.; Campbell M.; Taron C.H.; Rudd P.M. (2016). "Quantitative profiling of glycans and glycopeptides: an informatics' perspective". Current Opinion in Structural Biology. 40: 70–80. doi:10.1016/j.sbi.2016.07.022. PMID 27522273.

Ranzinger R.; York W.S. (2015). "GlycomeDB". Glycoinformatics. Methods in Molecular Biology. Vol. 1273. pp. 109–124. doi:10.1007/978-1-4939-2343-4_8. ISBN 978-1-4939-2342-7. PMID 25753706.

Ranzinger R.; Herget S.; von der Lieth C.-W.; Frank M. (2011). "GlycomeDB - a unified database for carbohydrate structures". Nucleic Acids Research. 39 (Database issue): D373-376. doi:10.1093/nar/gkq1014. PMC 3013643. PMID 21045056.

Aoki-Kinoshita K.F.; et al. (2016). "GlyTouCan 1.0 - The international glycan structure repository". Nucleic Acids Research. 44 (D1): D1237-1242. doi:10.1093/nar/gkv1041. PMC 4702779. PMID 26476458.

Campbell M.P.; Ranzinger R.; Lütteke T.; Mariethoz J.; Hayes CA.; Zhang J.; Akune Y.; Aoki-Kinoshita K.F.; Damerell D.; Carta G.; York W.S.; Haslam S.M.; Narimatsu H.; Rudd P.M.; Karlsson N.G.; Packer N.H.; Lisacek F. (2014). "Toolboxes for a standardised and systematic study of glycans". BMC Bioinformatics. 15 (Suppl 1): Suppl 1:S9. doi:10.1186/1471-2105-15-S1-S9. PMC 4016020. PMID 24564482.

Ranzinger R.; Herget S.; Wetter T.; von der Lieth C.-W. (2008). "GlycomeDB - integration of open-access carbohydrate structure databases". BMC Bioinformatics. 9: ID 384. doi:10.1186/1471-2105-9-384. PMC 2567997. PMID 18803830.

Toukach Ph.V.; Joshi H.; Ranzinger R.; Knirel Y.; von der Lieth C.-W. (2007). "Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de". Nucleic Acids Research. 35 (Database issue): D280 – D286. doi:10.1093/nar/gkl883. PMC 1899093. PMID 17202164.

Toukach Ph.V.; Egorova K.S. (2020). "New features of CSDB Linear, as compared to other carbohydrate notations". Journal of Chemical Information and Modeling. 60 (3): 1276–1289. doi:10.1021/acs.jcim.9b00744. PMID 31790229. S2CID 226214957.

Varki A.; et al. (2015). "Symbol Nomenclature for Graphical Representations of Glycans". Glycobiology. 25 (12): 1323–1324. doi:10.1093/glycob/cwv091. PMC 4643639. PMID 26543186.

Loss A.; Bunsmann P.; Bohne A.; Loss A.; Schwarzer E.; Lang E.; von der Lieth C.-W. (2002). "SWEET-DB: an attempt to create annotated data collections for carbohydrates". Nucleic Acids Research. 30 (1): 405–408. doi:10.1093/nar/30.1.405. PMC 99123. PMID 11752350.

Herget S.; Ranzinger R.; Maass K.; von der Lieth C.-W. (2008). "GlycoCT - a unifying sequence format for carbohydrates". Carbohydrate Research. 343 (12): 2162–2171. doi:10.1016/j.carres.2008.03.011. PMID 18436199.

Tanaka K.; Aoki-Kinoshita K.F.; Kotera M.; Sawaki H.; Tsuchiya S.; Fujita N.; Shikanai T.; Kato M.; Kawano S.; Yamada I.; Narimatsu H. (2014). "WURCS: the Web3 unique representation of carbohydrate structures". Journal of Chemical Information and Modeling. 54 (6): 1558–1566. doi:10.1021/ci400571e. PMID 24897372.

Kirschner K.N.; Yongye A.B.; Tschampel S.M.; González-Outeiriño J.; Daniels C.R.; Foley B.L.; Woods R.J. (2008). "GLYCAM06: a generalizable biomolecular force field. Carbohydrates". Journal of Computational Chemistry. 29 (4): 622–655. doi:10.1002/jcc.20820. PMC 4423547. PMID 17849372.

Ranzinger R.; Aoki-Kinoshita K.F.; Campbell M.P.; Kawano S.; Lütteke T.; Okuda S.; Shinmachi D.; Shikanai T.; Sawaki H.; Toukach Ph.V.; Matsubara M.; Yamada I.; Narimatsu H. (2015). "GlycoRDF: An ontology to standardize Glycomics data in RDF". Bioinformatics. 31 (6): 919–925. doi:10.1093/bioinformatics/btu732. PMC 4380026. PMID 25388145.

Aoki-Kinoshita K.F.; Bolleman J.; Campbell M.P.; Kawano S.; Kim J.; Lütteke T.; Matsubara M.; Okuda S.; Ranzinger R.; Sawaki H.; Shikanai T.; Shinmachi D.; Suzuki Y.; Toukach Ph.V.; Yamada I.; Packer N.H.; Narimatsu H. (2013). "Introducing glycomics data into the Semantic Web". Journal of Biomedical Semantics. 4 (1): ID 39. doi:10.1186/2041-1480-4-39. PMC 4177142. PMID 24280648.

nih.gov

pubmed.ncbi.nlm.nih.gov

Kapaev R.R.; Toukach Ph.V. (2018). "GRASS: semi-automated NMR-based structure elucidation of saccharides". Bioinformatics. 34 (6): 957–963. doi:10.1093/bioinformatics/btx696. PMID 29092007.

Toukach Ph.V.; Egorova K.S. (2017). "CSDB_GT: a new curated database on glycosyltransferases". Glycobiology. 27 (4): 285–290. doi:10.1093/glycob/cww137. PMID 28011601.

Egorova K.S.; Knirel Y.A.; Toukach Ph.V. (2019). "Expanding CSDB_GT glycosyltransferase database with Escherichia coli". Glycobiology. 29 (4): 285–287. doi:10.1093/glycob/cwz006. PMID 30759212.

Doubet S.; Albersheim P. (1992). "CarbBank". Glycobiology. 2 (6): 505–507. doi:10.1093/glycob/2.6.505. PMID 1472756.

Egorova K.S.; Toukach Ph.V. (2012). "Critical analysis of CCSD data quality". Journal of Chemical Information and Modeling. 52 (11): 2812–2814. doi:10.1021/ci3002815. PMID 23025661.

Egorova K.S.; Toukach Ph.V. (2013). "Expansion of coverage of Carbohydrate Structure Database (CSDB)". Carbohydrate Research. 389: 112–114. doi:10.1016/j.carres.2013.10.009. PMID 24680503.

Lütteke T. (2012). "The use of glycoinformatics in glycochemistry". Beilstein Journal of Organic Chemistry. 8: 915–929. doi:10.3762/bjoc.8.104. PMC 3388882. PMID 23015842.

Zhulin I.B. (2015). "Databases for Microbiologists". Journal of Bacteriology. 197 (15): 2458–2467. doi:10.1128/JB.00330-15. PMC 4505447. PMID 26013493.

Ranzinger R.; York W.S. (2015). "GlycomeDB". Glycoinformatics. Methods in Molecular Biology. Vol. 1273. pp. 109–124. doi:10.1007/978-1-4939-2343-4_8. ISBN 978-1-4939-2342-7. PMID 25753706.

Varki A.; et al. (2015). "Symbol Nomenclature for Graphical Representations of Glycans". Glycobiology. 25 (12): 1323–1324. doi:10.1093/glycob/cwv091. PMC 4643639. PMID 26543186.

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Carbohydrate Structure Database (English Wikipedia)

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