A quantitative structure-activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins

Glycobiology

Volumn 22, Issue 4, 2012, Pages 552-560

  Xuan, Pengfei ^a   Zhang, Yuehua ^a   Tzeng, Tzuen Rong Jeremy ^b   Wan, Xiu Feng ^c   Luo, Feng ^a  

^a Clemson University   (United States)

^b CLEMSON UNIVERSITY   (United States)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

glycan array; PLS; QSAR

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; DISACCHARIDE; GLYCAN BINDING PROTEIN; MONOSACCHARIDE; TETRASACCHARIDE; TRISACCHARIDE; UNCLASSIFIED DRUG;

ARTICLE; BINDING KINETICS; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN CARBOHYDRATE INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

ALGORITHMS; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; ONLINE SYSTEMS; PLANT LECTINS; POLYSACCHARIDES; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REGRESSION ANALYSIS; SOFTWARE;

EID: 84863246476     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwr163     Document Type: Article

References (20)

1. Alkhalil A, Achur RN, Valiyaveettil M, Ockenhouse CF, Gowda DC. 2000. Structural requirements for the adherence of plasmodium falciparum-infected erythrocytes to chondroitin sulfate proteoglycans of human placenta. J Biol Chem. 275:40357-40364. (Pubitemid 32064669)
2. Blixt O, Head S, Mondala T, Scanlan C, Huflejt ME, Alvarez R, Bryan MC, Fazio F, Calarese D, Stevens J. 2004. Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci USA. 101:17033.
3. Chandrasekaran A, Srinivasan A, Raman R, Viswanathan K, Raguram S, Tumpey TM, Sasisekharan V, Sasisekharan R. 2008. Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin. Nat Biotechnol. 26:107-113.
4. Chong IG, Jun CH. 2005. Performance of some variable selection methods when multicollinearity is present. Chemometr Intell Lab Syst. 78:103-112.
5. Dennis JW, Granovsky M, Warren CE. 1999. Protein glycosylation in development and disease. BioEssays. 21:412-421. (Pubitemid 29223313)
6. Drickamer K, Taylor ME. 2002. Glycan arrays for functional glycomics. Genome Biol. 3:1034.
7. Dube DH, Bertozzi CR. 2005. Glycans in cancer and inflammation-potential for therapeutics and diagnostics. Nat Rev Drug Discov. 4:477-488. (Pubitemid 40861990)
8. Fuster MM, Esko JD. 2005. The sweet and sour of cancer: Glycans as novel therapeutic targets. Nat Rev Cancer. 5:526-542. (Pubitemid 40942829)
9. Kuboyama T, Hirata K, Aoki-Kinoshita KF, Kashima H, Yasuda H. 2006. A gram distribution kernel applied to glycan classification and motif extraction. Genome Inform Ser. 17:25.
10. Lau KS, Dennis JW. 2008. N-Glycans in cancer progression. Glycobiology. 18:750-760.
11. Lin X. 2004. Functions of heparan sulfate proteoglycans in cell signaling during development. Development. 131:6009-6021. (Pubitemid 40123916)
12. Liu J, Shriver Z, Pope RM, Thorp SC, Duncan MB, Copeland RJ, Raska CS, Yoshida K, Eisenberg RJ, Cohen G, et al. 2002. Characterization of a heparan sulfate octasaccharide that binds to herpes simplex virus type 1 glycoprotein D. J Biol Chem. 277:33456-33467. (Pubitemid 34984869)
13. Perrimon N, Bernfield M. 2000. Specificities of heparan sulphate proteoglycans in developmental processes. Nature. 404:725-728. (Pubitemid 30212391)
14. Porter A, Yue T, Heeringa L, Day S, Suh E, Haab BB. 2010. A motif-based analysis of glycan array data to determine the specificities of glycanbinding proteins. Glycobiology. 20:369.
15. Stevens J, Blixt O, Glaser L, Taubenberger JK, Palese P, Paulson JC, Wilson IA. 2006. Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol. 355:1143-1155. (Pubitemid 43012153)
16. Taylor ME, Drickamer K. 2009. Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands. Glycobiology. 19:1155.
17. Varki A, et al. 1999. Essentials of Glycobiology, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
18. Wold S, Sjöström M, Eriksson L. 2001. PLS-regression: A basic tool of chemometrics. Chemometrics Intell Lab Syst. 58:109-130. (Pubitemid 33033283)
19. Wu CY, Liang PH, Wong CH. 2009. New development of glycan arrays. Org Biomol Chem. 7:2247-2254.
20. Yamanishi Y, Bach F, Vert JP. 2007. Glycan classification with tree kernels. Bioinformatics. 23:1211.