Glycoconjugate Data Bank:Structures - An annotated glycan structure database and N -glycan primary structure verification service

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Nakahara, Taku ^a   Hashimoto, Ryo ^a,d   Nakagawa, Hiroaki ^b   Monde, Kenji ^a   Miura, Nobuaki ^c   Nishimura, Shin Ichiro ^a  

^a Laboratory of Advanced Chemical Biology

^b Laboratory of Glyco Fine Chemistry

^c HOKKAIDO UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCAN;

ARTICLE; CARBOHYDRATE ANALYSIS; CLIENT SERVER APPLICATION; COMPUTER INTERFACE; COMPUTER PROGRAM; FACTUAL DATABASE; GLYCOCONJUGATE DATA BANK:STRUCTURES; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; DATABASES, FACTUAL; DATABASES, PROTEIN; GLYCOCONJUGATES; GLYCOPROTEINS; INTERNET; POLYSACCHARIDES; USER-COMPUTER INTERFACE;

EID: 38549146892     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm833     Document Type: Article

References (15)

1. Berman, H., Henrick, K. and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980.
2. Petrescu, A.J., Petreseu, S.M., Dwek, R.A. and Wormald, M.R. (1999) A statistical analysis of N- and O-glycan linkage conformations from crystallographic data. Glycobiology, 9, 343-352.
3. Wormald, M.R., Petrescu, A.J., Pao, Y.L., Glithero, A., Elliott, T. and Dwek, R.A. (2002) Conformational studies of oligosaccharides and glycopeptides: Complementarity of NMR, X-ray crystallography, and molecular modelling. Chem. Rev., 102, 371-386.
4. Lutteke, T., Frank, M. and von der Lieth, C.W. (2004) Data mining the protein data bank: Automatic detection and assignment of carbohydrate structures. Carbohydr. Res., 339, 1015-1020.
5. Lutteke, T. and von der Lieth, C.W. (2004) pdb-care (PDB carbohydrate residue check): A program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics, 5, 69.
6. Crispin, M., Stuart, D.I. and Jones, E.Y. (2007) Building meaningful models of glycoproteins. Nat. Struct. Mol. Biol., 14, 354.
7. Nakahara, T., Nishimura, S.I. and Shirai, T. (2007). Current aspects of carbohydrate structural bioinformatics, Curr. Chem. Biol., 1 265-270,
8. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T. and Kanehisa, M. (2006) KEGG as a glycome informatics resource. Glycobiology, 16, 63R-70R.
9. McNaught, A.D. (1996) Nomenclature of carbohydrates (IUPAC recommendations 1996). Pure Appl. Chem., 68, 1919-2008.
10. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M. and Hirakawa, M. (2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., 34, D354-D357.
11. Yamaguchi, A., Iida, K., Matsui, N., Tomoda, S., Yura, K. and Go, M. (2004) Het-PDB Navi.: A database for protein-small molecule interactions. J. Biochem., 135, 79-84.
12. Berman, H.M., Henrick, K., Nakamura, H. and Markley, J. (2007) Reply to: building meaningful models of glycoproteins. Nat. Struct. Mol. Biol. 14, 354-355.
13. Bohne-Lang, A., Lang, E., Forster, T. and von der Lieth, C.W. (2001) LINUCS: Linear notation for unique description of carbohydrate sequences. Carbohydr. Res., 336, 1-11.
14. Kikuchi, N., Kameyama, A., Nakaya, S., Ito, H., Sato, T., Shikanai, T., Takahashi, Y. and Narimatsu, H. (2005) The carbohydrate sequence markup language (CabosML): An XML description of carbohydrate structures. Bioinformatics, 21, 1717-1718.
15. Sahoo, S.S., Thomas, C., Sheth, A., Henson, C. and York, W.S. (2005) GLYDE-an expressive XML standard for the representation of glycan structure. Carbohydr. Res., 340, 2802-2807.