Data mining the PDB for glyco-related data

Methods in Molecular Biology

Volumn 534, Issue , 2009, Pages 293-310

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

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

3D structure; Bioinformatics; Glycoprotein; Glycosylation; Protein carbohydrate interaction; Torsion angle

Indexed keywords

CARBOHYDRATE; GLYCOPROTEIN;

ALGORITHM; ANIMAL; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; HUMAN; INFORMATION RETRIEVAL; METHODOLOGY; PROTEIN DATABASE; REVIEW;

ALGORITHMS; ANIMALS; CARBOHYDRATES; DATABASES, PROTEIN; GLYCOPROTEINS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR CONFORMATION; SOFTWARE;

EID: 66149104749     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-022-5_21     Document Type: Article

References (21)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (Pubitemid 30047768)
2. Petrescu, A.J., Petrescu, 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 (Pubitemid 29182150)
3. Lütteke, T., Bohne-Lang, A., Loss, A., Goetz, T., Frank, M., and von der Lieth, C.W. (2006) GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16, 71R-81R
4. Apweiler, R., Hermjakob, H., and Sharon, N. (1999) On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys. Acta 1473, 4-8
5. Imberty, A. and Pérez, S. (1995) Stereochemistry of the N-glycosylation sites in glycopro-teins. Protein Eng. 8, 699-709
6. Lütteke, T. and von der Lieth, C.W. (2006) The protein data bank (PDB) as a versatile resource for glycobiology and glycomics. Bio-catal Biotransformation 24, 147-155 (Pubitemid 43771955)
7. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., and Schneider, M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370 (Pubitemid 36157284)
8. Doubet, S., Bock, K., Smith, D., Darvill, A., and Albersheim, P. (1989) The complex carbohydrate structure database. Trends Biochem. Sci. 14, 475-477 (Pubitemid 19284340)
9. Lütteke, 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 (Pubitemid 38316974)
10. Bohne, A., Lang, E., and von der Lieth, C.W. (1999) SWEET-WWW-based rapid 3D construction of oligo-and polysaccharides. Bioin-formatics 15, 767-768 (Pubitemid 29484341)
11. 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 (Pubitemid 32995898)
12. Lütteke, 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
13. Lütteke, T., Frank, M., and von der Lieth, C.W. (2005) Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the Protein Data Bank. Nucleic Acids Res. 33, D242-D246 (Pubitemid 40207870)
14. Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95-99
15. Hooft, R.W., Sander, C., and Vriend, G. (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci. 13, 425-430 (Pubitemid 27384626)
16. Wormald, M.R., Petrescu, A.J., Pao, Y.L., Glithero, A., Elliott, T., and Dwek, R.A. (2002) Conformational studies of oligosac-charides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modeling. Chem. Rev. 102, 371-386 (Pubitemid 35377620)
17. Julenius, K., Molgaard, A., Gupta, R., and Brunak, S. (2005) Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15, 153-164 (Pubitemid 40227920)
18. Marshall, R. (1972) Glycoproteins. Annu. Rev. Biochem. 41, 673-702
19. Ben-Dor, S., Esterman, N., Rubin, E., and Sharon, N. (2004) Biases and complex patterns in the residues flanking protein N-glyco-sylation sites. Glycobiology 14, 95-101 (Pubitemid 38263094)
20. Petrescu, A.J., Milac, A.L., Petrescu, S.M., Dwek, R.A., and Wormald, M.R. (2004) Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure and folding. Glycobiology 14, 103-114 (Pubitemid 38263095)
21. Gavel, Y. and von Heijne, G. (1990) Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering. Protein Eng. 3, 433-442 (Pubitemid 20201068)