The protein data bank (PDB) as a versatile resource for glycobiology and glycomics

Biocatalysis and Biotransformation

Volumn 24, Issue 1-2, 2006, Pages 147-155

  Lütteke, Thomas ^a   Von Der Lieth, Claus W ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Carbohydrate; Glycobioinformatics; Glycobiology; Glycomics; Protein carbohydrate interactions

Indexed keywords

AMINO ACIDS; ATOMS; CONFORMATIONS; MASS SPECTROMETRY; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS;

CARBOHYDRATE STRUCTURE SUITE; GLYCOBIOLOGY; GLYCOMIC; PROTEIN DATA BANK;

CARBOHYDRATES;

GLYCAN DERIVATIVE; N ACETYLGLUCOSAMINE;

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; BIOINFORMATICS; CARBOHYDRATE ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; GLYCOBIOLOGY; GLYCOSYLATION; INFORMATION RETRIEVAL; INTERNET; MASS SPECTROMETRY; NOMENCLATURE; NUCLEAR MAGNETIC RESONANCE; ONLINE SYSTEM; PROTEIN CARBOHYDRATE INTERACTION; PROTEIN CONFORMATION; PROTEIN DATA BANK; RELIABILITY;

EID: 33646853740     PISSN: 10242422     EISSN: 10292446     Source Type: Journal    
DOI: 10.1080/10242420600598269     Document Type: Article

References (31)

1. Allen, FH. (2002) The Cambridge Structural Database: A quarter of a million crystal structures and rising Acta Crystallogr B, 58, pp. 380-388.
2. Berman, HM and Westbrook, J and Feng, Z and Gilliland, G and Bhat, TN and Weissig, H and Shindyalov, IN and Bourne, PE. (2000) The Protein Data Bank Nucleic Acids Res, 28, pp. 235-242.
3. Bohne, A and Lang, E and von der Lieth, CW. (1999) SWEET-WWW-based rapid 3D construction of oligo- and polysaccharides Bioinformatics, 15, pp. 767-768.
4. Bohne-Lang, A and Lang, E and Forster, T and von der Lieth, CW. (2001) LINUCS: Linear notation for unique description of carbohydrate sequences Carbohydr Res, 336, pp. 1-11.
5. Bohne-LangA, von der LiethCW. 2005. GlyProt: Is silico glycosylation of proteins. Nucleic Acids Res 33:214-219.
6. Dwek, RA and Butters, TD and Platt, FM and Zitzmann, N. (2002) Targeting glycosylation as a therapeutic approach Nat Rev Drug Discov, 1, pp. 65-75.
7. Feizi, T and Mulloy, B. (2003) Carbohydrates and glycoconjugates. Glycomics: The new era of carbohydrate biology Curr Opin Struct Biol, 13, pp. 602-604.
8. Feizi, T and Chai, W. (2004) Oligosaccharide microarrays to decipher the glyco code Nat Rev Mol Cell Biol, 5, pp. 582-588.
9. Frank, M and Bohne-Lang, A and Wetter, T and von der Lieth, CW. (2002) Rapid generation of a representative ensemble of N-glycan conformations In Silico Biol, 2, pp. 427-439.
10. Gabius, HJ and Siebert, HC and Andre, S and Jimenez-Barbero, J and Rudiger, H. (2004) Chemical biology of the sugar code Chembiochem, 5, pp. 740-764.
11. GotzT, Bohne-LangA, FrankM, LohmannK, LossA, LüttekeT, von der LiethCW. 2004. glycosciences.de: An Internet Portal for Glyco-related Data from Open Access Resources, In: R.a.S.Giegerich, J., editor. German Conference on Bioinformatics, 2004Bonn: Köllen Druck+Verlag GmbH. p 115-9.
12. Imberty, A and Perez, S. (1995) Stereochemistry of the N-glycosylation sites in glycoproteins Protein Eng, 8, pp. 699-709.
13. Imberty, A and Perez, S. (2000) Structure, conformation, and dynamics of bioactive oligosaccharides: Theoretical approaches and experimental validations Chem Rev, 100, pp. 4567-4588.
14. Kogelberg, H and Feizi, T. (2003) New structural insights into lectin-type proteins of the immune system Curr Opin Struct Biol, 11, pp. 635-643.
15. Kogelberg, H and Solis, D and Jimenez-Barbero, J. (2003) New structural insights into carbohydrate-protein interactions from NMR spectroscopy Curr Opin Struct Biol, 13, pp. 646-653.
16. Lehmann, WD and Bohne, A and von der Lieth, CW. (2000) The information encrypted in accurate peptide masses-improved protein identification and assistance in glycopeptide identification and characterization J Mass Spectrom, 35, pp. 1335-1341.
17. Loris, R. (2002) Principles of structures of animal and plant lectins Biochim Biophys Acta, 1572, pp. 198-208.
18. Loss, A and Bunsmann, P and Bohne, A and Loss, A and Schwarzer, E and Lang, E and von der Lieth, CW. (2002) SWEET-DB: An attempt to create annotated data collections for carbohydrates Nucleic Acids Res, 30, pp. 405-408.
19. Lütteke, T and Frank, M and von der Lieth, CW. (2004) Data mining the protein data bank: Automatic detection and assignment of carbohydrate structures Carbohydr Res, 339, pp. 1015-1020.
20. LüttekeT, von der LiethCW. 2004. Pdb-care (PDB carbohydrate residue check): A program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics 5:69.
21. Lütteke, T and Frank, M and von der Lieth, CW. (2005) Carbohydrate Structure Suite (CSS): Analysis of carbohydrate 3D structures derived from the PDB Nucleic Acids Res, 33, pp. D242-D246.
22. Petrescu, AJ and Petrescu, SM and Dwek, RA and Wormald, MR. (1999) A statistical analysis of N- and O-glycan linkage conformations from crystallographic data Glycobiology, 9, pp. 343-352.
23. Petrescu, AJ and Milac, AL and Petrescu, SM and Dwek, RA and Wormald, MR. (2004) Statistical analysis of the protein environment of N-glycosylation sites: Implications for occupancy, structure and folding Glycobiology, 14, pp. 103-114.
24. Pratt, MR and Bertozzi, CR. (2005) Synthetic glycopeptides and glycoproteins as tools for biology Chem Soc Rev, 34, pp. 58-68.
25. Ratner, DM and Adams, EW and Disney, MD and Seeberger, PH. (2004) Tools for glycomics: Mapping interactions of carbohydrates in biological systems Chembiochem, 5, pp. 1375-1383.
26. Sharma, V and Surolia, A. (1997) Analyses of carbohydrate recognition by legume lectins: Size of the combining site loops and their primary specificity J Mol Biol, 267, pp. 433-445.
27. Sharon, N and Lis, H. (2001) The structural basis for carbohydrate recognition by lectins Adv Exp Med Biol, 491, pp. 1-16.
28. Taroni, C and Jones, S and Thornton, JM. (2000) Analysis and prediction of carbohydrate binding sites Protein Eng, 13, pp. 89-98.
29. Varki, A and Cummings, R and Esko, J and Freeze, H and Hart, G and Marth, J.(1999) Essentials of Glycobiology. New York: Cold Spring Harbor Laboratory Press.
30. WerzDB, SeebergerPH. 2005. Carbohydrates as the Next Frontier in Pharmaceutical Research. Chemistry.
31. Woods, RJ. (1998) Computational carbohydrate chemistry: What theoretical methods can tell us Glycoconj J, 15, pp. 209-216.