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Advances in Bioinformatics
Volume 2010 (2010), Article ID 289301, 9 pages
Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines
1Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
2Agricultural Bioinformatics Research Unit, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
Received 6 March 2010; Revised 20 May 2010; Accepted 19 July 2010
Academic Editor: Rita Casadio
Copyright © 2010 Seizi Someya et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- N. Sharon and H. Lis, Lectins, Springer, Dordrecht, The Netherlands, 2nd edition, 2003.
- V. Vapnik, Statistical Learning Theory, Wiley, New York, NY, USA, 1998.
- L. H. Wang, J. Liu, Y. F. Li, and H. B. Zhou, “Predicting protein secondary structure by a support vector machine based on a new coding scheme,” Genome Informatics Series, vol. 15, no. 2, pp. 181–190, 2004.
- J. J. Ward, J. S. Sodhi, L. J. McGuffin, B. F. Buxton, and D. T. Jones, “Prediction and functional analysis of native disorder in proteins from the three kingdoms of life,” Journal of Molecular Biology, vol. 337, no. 3, pp. 635–645, 2004.
- C. H. Q. Ding and I. Dubchak, “Multi-class protein fold recognition using support vector machines and neural networks,” Bioinformatics, vol. 17, no. 4, pp. 349–358, 2001.
- C. Shionyu-Mitsuyama, T. Shirai, H. Ishida, and T. Yamane, “An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins,” Protein Engineering, vol. 16, no. 7, pp. 467–478, 2003.
- A. Malik and S. Ahmad, “Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network,” BMC Structural Biology, vol. 7, article 1, 2007.
- C. Leslie, E. Eskin, and W. S. Noble, “The spectrum kernel: a string kernel for SVM protein classification,” in Proceedings of the Pacific Symposium on Biocomputing, pp. 564–575, 2002.
- A. K. Smith, K.-H. Cheung, and K. Y. Yip, “The Universal Protein Resource (UniProt),” Nucleic Acids Research, vol. 35, no. 1, pp. D193–D197, 2007.
- T. Endo, “Finding of O-mannosyl glycan in mammals and congenital muscular dystrophies due to glycosylation defects,” Yakugaku Zasshi, vol. 123, no. 10, pp. 825–835, 2003 (Japanese).
- Y. Kamiya, Y. Yamaguchi, and Y. Yamaguchi, “Sugar-binding properties of VIP36, an intracellular animal lectin operating as a cargo receptor,” The Journal of Biological Chemistry, vol. 280, no. 44, pp. 37178–37182, 2005.
- N. Sharon, “Lectins: carbohydrate-specific reagents and biological recognition molecules,” The Journal of Biological Chemistry, vol. 282, no. 5, pp. 2753–2764, 2007.
- E. Pyz, A. S. J. Marshall, S. Gordon, and G. D. Brown, “C-type lectin-like receptors on myeloid cells,” Annals of Medicine, vol. 38, no. 4, pp. 242–251, 2006.
- S. S. Deepa, Y. Umehara, S. Higashiyama, N. Itoh, and K. Sugahara, “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, vol. 277, no. 46, pp. 43707–43716, 2002.
- A. R. Aricescu, I. W. McKinnell, W. Halfter, and A. W. Stoker, “Heparan sulfate proteoglycans are ligands for receptor protein tyrosine phosphatase σ,” Molecular and Cellular Biology, vol. 22, no. 6, pp. 1881–1892, 2002.
- S. G. Kallapur and R. A. Akeson, “The neural cell adhesion molecule (NCAM) heparin binding domain binds to cell surface heparan sulfate proteoglycans,” Journal of Neuroscience Research, vol. 33, no. 4, pp. 538–548, 1992.
- P. S. Mohan, D. K. H. Chou, and F. B. Jungalwala, “Sulfoglucuronyl glycolipids bind laminin,” Journal of Neurochemistry, vol. 54, no. 6, pp. 2024–2031, 1990.
- G. J. Cole and R. Akeson, “Identification of a heparin binding domain of the neural cell adhesion molecule N-CAM using synthetic peptides,” Neuron, vol. 2, no. 2, pp. 1157–1165, 1989.
- C. Cebo, G. Vergoten, and J.-P. Zanetta, “Lectin activities of cytokines: functions and putative carbohydrate-recognition domains,” Biochimica et Biophysica Acta, vol. 1572, no. 2-3, pp. 422–434, 2002.
- G. Vergoten and J.-P. Zanetta, “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, vol. 24, no. 4-5, pp. 183–193, 2007.
- J. Parkkinen, E. Raulo, J. Merenmies, R. Nolo, E. O. Kajander, M. Baumann, and H. Rauvala, “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, vol. 268, no. 26, pp. 19726–19738, 1993.
- R. Apweiler, A. Gateau, and A. Gateau, “Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL,” in Proceedings of the International Conference on Intelligent Systems for Molecular Biology (ISMB '97), vol. 5, pp. 33–43, 1997.
- R. Apweiler, “Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences,” Briefings in Bioinformatics, vol. 2, no. 1, pp. 9–18, 2001.
- A. A. Schäffer, Y. I. Wolf, C. P. Ponting, E. V. Koonin, L. Aravind, and S. F. Altschul, “IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices,” Bioinformatics, vol. 15, no. 12, pp. 1000–1011, 1999.
- S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
- A. Marchler-Bauer, A. R. Panchenko, B. A. Shoemarker, P. A. Thiessen, L. Y. Geer, and S. H. Bryant, “CDD: a database of conserved domain alignments with links to domain three-dimensional structure,” Nucleic Acids Research, vol. 30, no. 1, pp. 281–283, 2002.
- M. Levitt, “Conformational preferences of amino acids in globular proteins,” Biochemistry, vol. 17, no. 20, pp. 4277–4285, 1978.
- J. M. Rini, “Lectin structure,” Annual Review of Biophysics and Biomolecular Structure, vol. 24, pp. 551–577, 1995.
- N. R. Chandra, M. M. Prabu, K. Suguna, and M. Vijayan, “Structural similarity and functional diversity in proteins containing the legume lectin fold,” Protein Engineering, vol. 14, no. 11, pp. 857–866, 2001.
- L. M. Wright, E. J. M. Van Damme, and E. J. M. Van Damme, “Isolation, characterization, molecular cloning and molecular modelling of two lectins of different specificities from bluebell (Scilla campanulata) bulbs,” Biochemical Journal, vol. 340, no. 1, pp. 299–308, 1999.
- T. W. Hamelryck, R. Loris, J. Bouckaert, and L. Wyns, “Structural features of the legume lectins,” Trends in Glycoscience and Glycotechnology, vol. 10, no. 55, pp. 349–360, 1998.
- G. Hester, H. Kaku, I. J. Goldstein, and C. S. Wright, “Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family,” Nature Structural Biology, vol. 2, no. 6, pp. 472–479, 1995.
- B. E. Torian, B. M. Flores, V. L. Stroeher, F. S. Hagen, and W. E. Stamm, “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, vol. 87, no. 16, pp. 6358–6362, 1990.
- T. Fawcett, “ROC graphs: notes and practical considerations for researchers,” HP Labs Technical Reports HPL-2003-4, HP Laboratories, Palo Alto, Calif, USA, 2004.
- 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, vol. 36, pp. D793–D799, 2008.