Acta Biotheoretica

, Volume 53, Issue 1, pp 39–47 | Cite as

Support Vector Machines for Predicting Apoptosis Proteins Types

  • Jing Huang
  • Feng Shi


Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death, and their function is related to their types. According to the classification scheme by Zhou and Doctor (2003), the apoptosis proteins are categorized into the following four types: (1) cytoplasmic protein; (2) plasma membrane-bound protein; (3) mitochondrial inner and outer proteins; (4) other proteins. A powerful learning machine, the Support Vector Machine, is applied for predicting the type of a given apoptosis protein by incorporating the sqrt-amino acid composition effect. High success rates were obtained by the re-substitute test (98/98 = 100 %) and the jackknife test (89/98 = 90.8%).

Key Words

support vector machine subcellular location sqrt-amino acid composition 


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  1. Barinaga, M. (1998). Stroke-damaged neurons may commit cellular suicide. Science 281: 1302–1303.CrossRefPubMedGoogle Scholar
  2. Cai, Y.D. and K.C. Chou (2003). Nearest neighbour algorithm for predicting protein subcellular location by combing functional domain composition and pseudo-amino acid composition. Biochemical and Biophysical Research Communications 305: 407–411.CrossRefPubMedGoogle Scholar
  3. Cai, Y.D., G.P. Zhou and K.C. Chou (2003). Support vector machine for predicting membrane protein types by using functional domine composition. Biophysical Journal 84: 3257–3263.PubMedGoogle Scholar
  4. Cai, Y.D., X.J. Liu and K.C. Chou (2001). Artificial neural network model for predicting membrane protein types. Journal of Biomolecular Stereodynamics 18: 607–610.Google Scholar
  5. Cai, Y.D., X.J. Liu, X.B. Xu and K.C. Chou (2000a). Support vector machines for prediction of protein subcellular location. Molecular Cell Biology Research Communications 4: 230–233.CrossRefGoogle Scholar
  6. Cai, Y.D., X.J. Liu, X.B. Xu and K.C. Chou (2000b). Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. Journal of Biological Chemistry 84: 343–348.Google Scholar
  7. Chou, J.J., H. Li, G.S. Salvesen, J. Yuan and G. Wagner (1999). Solution structure of BID, an intracellular amplifier of apoptotic signaling. Cell 96: 615–624.CrossRefPubMedGoogle Scholar
  8. Chou, K.C. (1995). A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Structure, Function and Genetics 21: 319–344.Google Scholar
  9. Chou, K.C. (1999). A key driving force in determination of protein structural classes. Biochemical and Biophysical Research Communications 264: 216–224.CrossRefPubMedGoogle Scholar
  10. Chou, K.C. (2000a). Prediction of protein subcellular locations by incorporation quasi-sequence-order effect. Bichemical and Biophysical Research Communication 19: 477–483.CrossRefGoogle Scholar
  11. Chou, K.C. (2000b). Review: Prediction of protein structural classes and subcellular location. Current Protein and Peptide Science 1: 171–208.CrossRefGoogle Scholar
  12. Chou, K.C. (2001). Prediction of protein cellular attributes using pseudo-amino-acid-composition. Proteins: Structure, Function, and Genetics 43: 246–255.Google Scholar
  13. Chou, K.C. and Y.D. Cai (2002). Using functional domain composition and support vector machines for prediction of protein subcellular location. Journal of Biology Chemistry 277: 45765–45769.CrossRefGoogle Scholar
  14. Chou, K.C. and Y.D. Cai (2003a). A new hybrid approach to predict subcellular localization of proteins by incorporating Gene ontology. Bichemical and Biophysical Research Communication 311: 743–747.CrossRefGoogle Scholar
  15. Chou, K.C. and Y.D. Cai (2003b). Predication and classification of protein subcellular location:sequence-order effect and pseudo amino composition. Journal of Cellular Biochemistry 90: 1250–1260.CrossRefGoogle Scholar
  16. Chou, K.C. and D.W. Elrod (1999a). Prediction of membrane protein types and subcellular locations. Proteins 34: 137–153.CrossRefGoogle Scholar
  17. Chou, K.C. and D.W. Elrod (1999b). Protein subcellular location prediction. Protein Engineering 12: 107–118.CrossRefGoogle Scholar
  18. Chou, K.C., D. Jones and R.L. Heinrikson (1997). Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Letters 419: 49–54.CrossRefPubMedGoogle Scholar
  19. Chou, K.C. and G.M. Maggiora (1998). Domain structural class prediction. Protein Engineering 11: 523–538.CrossRefPubMedGoogle Scholar
  20. Chou, K.C., A.G. Tomasselli and R.L. Heinrikson (2000). Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Letters 470: 249–256.CrossRefPubMedGoogle Scholar
  21. Chou, K.C. and C.T. Zhang (1994). Review: Predicting protein folding types by distance functions that make allowances for amino acid interactions. Journal of Biological Chemistry 269: 22014–22020.PubMedGoogle Scholar
  22. Chou, K.C. and C.T. Zhang (1995). Prediction of protein structural classes. Critical Reviews in Biochemistry and Molecular Biology 30: 275–349.PubMedGoogle Scholar
  23. Cortes, C. and V. Vapnik (1995). Support vector networks. Machine Learning 20: 273–293.Google Scholar
  24. Ding, C.H. and I. Dubchak (2001). Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17: 349–358.CrossRefPubMedGoogle Scholar
  25. Evan, G. and T. Littlewood (1998). A matter of life and cell death. Science 281: 1317–1322.CrossRefPubMedGoogle Scholar
  26. Feng, Z.P. (2001). Prediction of the subcellular location of prokaryotic proteins based on a new representation of the amino acid composition. Biopolymers 58: 491–499.CrossRefPubMedGoogle Scholar
  27. Hua, S.J. and Z.R. Sun (2001a). Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17: 721–728.CrossRefGoogle Scholar
  28. Hua, S.J. and Z.R. Sun (2001b). A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach. Journal of Molecular Biology 308: 397–407.CrossRefGoogle Scholar
  29. Jacobson, M.D., M. Weil and M.C. Raff (1997). Programmed cell death in animal development. Cell 88: 347–354.PubMedGoogle Scholar
  30. Kerr, J.F., A.H. Wyllie and A.R. Currie (1972). Apoptosis: A basic biological phenomenon with wide-ranging implications in tissue kinetics. British Journal of Cancer 26: 239–257.PubMedGoogle Scholar
  31. Pan, Y.X., Z.Z. Zhang, Z.M. Guo, G.Y. Feng, Z.D. Huang and L. He (2003). Application of pseudo amino acid composition for predicting protein subcellular location: Stochastic signal processing approach. Journal of Protein Chemistry 22: 395–402.CrossRefPubMedGoogle Scholar
  32. Reed, J.C. and G. Paternostro (1999). Postmitochondrial regulation of apoptosis during heart failure. Proceedings of the National Academy of Sciences 96: 7614–7616.CrossRefGoogle Scholar
  33. Schulz, J.B., M. Weller and M.A. Moskowitz (1999). Caspases as treatment targets in stroke and neurodegenerative diseases. Annals of Neurology 45: 421–429.CrossRefPubMedGoogle Scholar
  34. Suzuki, M., R.J. Youle and N. Tjandra (2000). Structure of Bax: Coregulation of dimer formation and intracellular location. Cell 103: 645–654.CrossRefPubMedGoogle Scholar
  35. Vapnik, V. (1998). Statistical Learning Theory. Wiley Interscience, New York.Google Scholar
  36. Zhang, S.W., Q. Pan, H.C. Zhang, Y.L. Zhang and H.Y. Wang (2003). Classification of protein quaternary structure with support vector machine, Bioinformatics 19: 2390–2396.CrossRefPubMedGoogle Scholar
  37. Zhao, Y.D., C. Pinilla, D. Valmori, R. Martin and R. Simon (2003). Application of support vector machines for T-cell epitopes prediction, Bioinformatics 19: 1978–1984.CrossRefPubMedGoogle Scholar
  38. Zhou, G.P. (1998). An intriguing controversy over protein structural class prediction. Journal of Protein Chemistry 17: 729–738.CrossRefPubMedGoogle Scholar
  39. Zhou, G.P. and N. Assa-Munt (2001). Some insights into protein structural class prediction. Proteins: Structure, Function, and Genetics 44: 57–59.Google Scholar
  40. Zhou, G.P. and K. Doctor (2003). Subcelluar location of Apoptosis proteins. Proteins: Structure, Function, and Genetic 50: 44–48.Google Scholar
  41. Zhou, P., J. Chou, R.S. Olea, J. Yuan and G. Wagner (1999). Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: A structural basis for specific adaptor/caspase interaction. Proceedings of the National Academy of Sciences 96: 11265–11270.CrossRefGoogle Scholar

Copyright information

© Springer Science + Business Media, Inc. 2005

Authors and Affiliations

  1. 1.School of ComputerWuhan UniversityWuhanPR China
  2. 2.School of ScienceHuazhong Agricultural UniversityWuhanPR China
  3. 3.School of Mathematics and StatisticsWuhan UniversityWuhanPR China

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