Automatic Spectrum Interpretation Based on Increment Rules: CASPER

Bioinformatics for Glycobiology and Glycomics: An Introduction

Volumn , Issue , 2009, Pages 311-320

  Stenutz, Roland ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Carbohydrate; Chemical shift prediction; Glycoside; NMR; Oligosaccharide; Polysaccharide; Structure prediction

Indexed keywords

EID: 79952567191     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470029619.ch16     Document Type: Chapter

References (27)

1. Bremser W: Expectation ranges of 13C NMR chemical shifts. Magn Resonan Chem 1985, 23: 271-275.
2. Búrgin Schaller R, Munk ME, Pretsch E: Spectra estimation for computer-aided structure determination. J Chem Inf Comput Sci 1996, 36: 239-243.
3. Pretsch E, Fúrst A, Badertscher M, Búrgin R: C13Shift: a computer program for the prediction of 13C NMR spectra based on an open set of additivity rules. J Chem Inf Comput Sci 1992, 32: 291-295.
4. Steinbeck C, Kuhn S: NMRShiftDB -compound identification and structure elucidation support through a free community-built web database. Phytochemistry 2004, 65:2711-2717.
5. Satoh H, Koshino H, Uzawa J, Nakata T: CAST/CNMR: highly accurate 13C NMR chemical shift prediction system considering stereochemistry. Tetrahedron 2003, 59:4539-4547.
6. Schútz V, Purtuc V, Felsinger S, Robien W: CSEARCH-STEREO: a new generation of NMR database systems allowing three-dimensional spectrum prediction. Fresenius' J Anal Chem 1997, 359:33-41.
7. Abraham R: A model for the calculation of proton chemical shifts in non-conjugated organic compounds. Prog Nucl Magn Reson Spectrosc 1999, 35:85-152.
8. de Dios A: Ab initio calculations of the NMR chemical shift. Prog Nucl Magn Reson Spectrosc 1996, 29:229-278.
9. Helgaker T, Jaszunski M, Ruud K: Ab initio methods for the calculation of NMR shielding and indirect spin-spin coupling constants. Chem Rev 1999, 99:293-352.
10. Mazeau K, Taravel F, Tvaroska I: Angular dependence of the C-6 chemical shift and the conformation of the hydroxymethyl group in carbohydrates. Chem Pap Chem Zvesti 1996, 50:77-83.
11. McIntyre M, Small G: Carbon-13 nuclear magnetic resonance spectrum simulation methodology for the structure elucidation of carbohydrates. Anal Chem 1987, 59:1805-1811.
12. Small G, McIntyre M: Structure elucidation methodology for disaccharides based on carbon-13 nuclear magnetic resonance spectrum simulation. Anal Chem 1989, 61:666-674.
13. Clouser D, Jurs P: Simulation of the 13C nuclear magnetic resonance spectra of trisaccharides using multiple linear regression analysis and neural networks. Carbohydr Res 1995, 271: 65-77.
14. Szilágyi L: Chemical shifts in proteins come of age. Prog Nucl Magn Reson Spectrosc 1995, 27:325-443.
15. Lemieux R, Koto S: The conformational properties of glycosidic linkages. Tetrahedron 1974, 30:1933-1944.
16. Kochetkov N, Chizhov O, Shashkov A: Dependence of 13C chemical shifts on the spatial interaction of protons, and its application in structural and conformational studies of oligo-and polysaccharide. Carbohydr Res 1984, 133:173-185.
17. Jansson P, Kenne L, Widmalm G: Casper -a computerised approach to structure determination of polysaccharides using information from n.m.r. spectroscopy and simple chemical analyses. Carbohydr Res 1987, 168:67-77.
18. Lipkind G, Shashkov A, Knirel Y, Vinogradov E, Kochetkov N: A computer-assisted structural analysis of regular polysaccharides on the basis of carbon-13 NMR data. Carbohydr Res 1988, 175:59-75.
19. Toukach F, Knirel Y: New database of bacterial carbohydrate structures. In XVIII International Symposium on Glycoconjugates, Florence, Italy; 2005, pp. 216-217.
20. Jansson P, Kenne L,Widmalm G: Computer-assisted structural analysis of polysaccharides with an extended version of casper using proton and carbon-13 NMR data. Carbohydr Res 1989: 169-191.
21. Jansson P, Kenne L, Widmalm G: CASPER: a computer program used for structural analysis of carbohydrates. J Chem Inf Comput Sci 1991, 31:508-516.
22. Jansson P, Stenutz R, Widmalm G: Sequence determination of oligosaccharides and regular polysaccharides using NMR spectroscopy and a novel web-based version of the computer program CASPER. Carbohydr Res 2006, 341:1003-1010.
23. Stenutz R, Jansson P, Widmalm G: Computer-assisted structural analysis of oligo-and polysaccharides: an extension of CASPER to multibranched structures. Carbohydr Res 1998, 306:11-17.
24. Toukach F, Shashkov A: Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data. Carbohydr Res 2001, 335:101-114.
25. Bock K, Pedersen C: Carbon-13 nuclear magnetic resonance spectroscopy of monosaccharides. Adv Carbohydr Chem Biochem 1983, 41:27-66.
26. Kornfeld R, Kornfeld S: Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 1985, 54:631-664.
27. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34: D354-D357.