Prediction of carbohydrate-binding proteins from sequences using support vector machines

Advances in Bioinformatics

Volumn 2010, Issue , 2010, Pages

  Shimizu, Kentaro ^a   Someya, Seizi ^a   Kakuta, Masanori ^a   Morita, Mizuki ^a   Sumikoshi, Kazuya ^a   Cao, Wei ^a   Ge, Zhenyi ^a   Hirose, Osamu ^a   Nakamura, Shugo ^a   Terada, Tohru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78349235041     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2010/289301     Document Type: Article

References (36)

1. Sharon N., Lis H., Lectins 2003 2nd Dordrecht, The Netherlands Springer
2. Vapnik V., Statistical Learning Theory 1998 New York, NY, USA Wiley
3. Wang L. H., Liu J., Li Y. F., Zhou H. B., Predicting protein secondary structure by a support vector machine based on a new coding scheme Genome Informatics Series 2004 15 2 181 190
4. Ward J. J., Sodhi J. S., McGuffin L. J., Buxton B. F., Jones D. T., Prediction and functional analysis of native disorder in proteins from the three kingdoms of life Journal of Molecular Biology 2004 337 3 635 645
5. Ding C. H. Q., Dubchak I., Multi-class protein fold recognition using support vector machines and neural networks Bioinformatics 2001 17 4 349 358
6. Shionyu-Mitsuyama C., Shirai T., Ishida H., Yamane T., An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins Protein Engineering 2003 16 7 467 478
7. Malik A., Ahmad S., Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network BMC Structural Biology 2007 7, article 1
8. Leslie C., Eskin E., Noble W. S., The spectrum kernel: a string kernel for SVM protein classification Proceedings of the Pacific Symposium on Biocomputing 2002 564 575
9. Smith A. K., Cheung K.-H., Yip K. Y., The Universal Protein Resource (UniProt) Nucleic Acids Research 2007 35 1 D193 D197
10. Endo T., Finding of O-mannosyl glycan in mammals and congenital muscular dystrophies due to glycosylation defects Yakugaku Zasshi 2003 123 10 825 835
11. Kamiya Y., Yamaguchi Y., Takahashi M., Arata Y., Kasai K.-I., Ihara Y., Matsuo I., Ito Y., Yamamoto K., Kato K., Sugar-binding properties of VIP36, an intracellular animal lectin operating as a cargo receptor The Journal of Biological Chemistry 2005 280 44 37178 37182
12. Sharon N., Lectins: carbohydrate-specific reagents and biological recognition molecules The Journal of Biological Chemistry 2007 282 5 2753 2764
13. Pyz E., Marshall A. S. J., Gordon S., Brown G. D., C-type lectin-like receptors on myeloid cells Annals of Medicine 2006 38 4 242 251
14. Deepa S. S., Umehara Y., Higashiyama S., Itoh N., Sugahara K., Specific molecular interactions of oversulfated chondroitin sulfate E with various heparin-binding growth factors: implications as a physiological binding partner in the brain and other tissues The Journal of Biological Chemistry 2002 277 46 43707 43716
15. Aricescu A. R., McKinnell I. W., Halfter W., Stoker A. W., Heparan sulfate proteoglycans are ligands for receptor protein tyrosine phosphatase Molecular and Cellular Biology 2002 22 6 1881 1892
16. Kallapur S. G., Akeson R. A., The neural cell adhesion molecule (NCAM) heparin binding domain binds to cell surface heparan sulfate proteoglycans Journal of Neuroscience Research 1992 33 4 538 548
17. Mohan P. S., Chou D. K. H., Jungalwala F. B., Sulfoglucuronyl glycolipids bind laminin Journal of Neurochemistry 1990 54 6 2024 2031
18. Cole G. J., Akeson R., Identification of a heparin binding domain of the neural cell adhesion molecule N-CAM using synthetic peptides Neuron 1989 2 2 1157 1165
19. Cebo C., Vergoten G., Zanetta J.-P., Lectin activities of cytokines: functions and putative carbohydrate-recognition domains Biochimica et Biophysica Acta 2002 1572 2-3 422 434
20. Vergoten G., Zanetta J.-P., Structural differences between the putative carbohydrate-recognition domains of human IL-1 alpha, IL-1 beta and IL-1 receptor antagonist obtained by in silico modeling Glycoconjugate Journal 2007 24 4-5 183 193
21. Parkkinen J., Raulo E., Merenmies J., Nolo R., Kajander E. O., Baumann M., Rauvala H., Amphoterin, the 30-kDa protein in a family of HMG1-type polypeptides. Enhanced expression in transformed cells, leading edge localization, and interactions with plasminogen activation The Journal of Biological Chemistry 1993 268 26 19726 19738
22. Apweiler R., Gateau A., Contrino S., Martin M. J., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Bairoch A., Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL 5 Proceedings of the International Conference on Intelligent Systems for Molecular Biology (ISMB '97) 1997 33 43
23. Apweiler R., Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences Briefings in Bioinformatics 2001 2 1 9 18
24. Schffer A. A., Wolf Y. I., Ponting C. P., Koonin E. V., Aravind L., Altschul S. F., IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices Bioinformatics 1999 15 12 1000 1011
25. Altschul S. F., Madden T. L., Schffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Research 1997 25 17 3389 3402
26. Thompson J. D., Higgins D. G., Gibson T. J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 1994 22 22 4673 4680
27. Marchler-Bauer A., Panchenko A. R., Shoemarker B. A., Thiessen P. A., Geer L. Y., Bryant S. H., CDD: a database of conserved domain alignments with links to domain three-dimensional structure Nucleic Acids Research 2002 30 1 281 283
28. Levitt M., Conformational preferences of amino acids in globular proteins Biochemistry 1978 17 20 4277 4285
29. Rini J. M., Lectin structure Annual Review of Biophysics and Biomolecular Structure 1995 24 551 577
30. Chandra N. R., Prabu M. M., Suguna K., Vijayan M., Structural similarity and functional diversity in proteins containing the legume lectin fold Protein Engineering 2001 14 11 857 866
31. Wright L. M., Van Damme E. J. M., Barre A., Allen A. K., Van Leuven F., Reynolds C. D., Rouge P., Peumans W. J., Isolation, characterization, molecular cloning and molecular modelling of two lectins of different specificities from bluebell (Scilla campanulata) bulbs Biochemical Journal 1999 340 1 299 308
32. Hamelryck T. W., Loris R., Bouckaert J., Wyns L., Structural features of the legume lectins Trends in Glycoscience and Glycotechnology 1998 10 55 349 360
33. Hester G., Kaku H., Goldstein I. J., Wright C. S., Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family Nature Structural Biology 1995 2 6 472 479
34. Torian B. E., Flores B. M., Stroeher V. L., Hagen F. S., Stamm W. E., cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica Proceedings of the National Academy of Sciences of the United States of America 1990 87 16 6358 6362
35. Fawcett T., ROC graphs: notes and practical considerations for researchers HP Labs Technical Reports 2004 HPL-2003-4 Palo Alto, Calif, USA HP Laboratories
36. Genome Information Integration Project and H-Invitational 2, The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts Nucleic Acids Research 2008 36 D793 D799