Applied Biochemistry and Biotechnology

, Volume 171, Issue 3, pp 590–615

Predictions of Enzymatic Parameters: A Mini-Review with Focus on Enzymes for Biofuel

Article

Abstract

Enzymatic reactions are very basic processes in biological systems, and parameters related to enzymatic reactions always provide good indicators for understanding of mechanisms underlined in enzymatic reactions, for better controlling of enzymatic reactions, and for comparison of different enzymes. In this mini-review: first, parameters in enzymatic reactions were briefly reviewed from three different standpoints; second, predictions of parameters in enzymatic reactions without information on enzyme structure were shortly reviewed from viewpoints of geometric approach, graphic approach and compartmental approach; third, predictions of parameters in enzymatic reaction with information on enzyme structure were reviewed from the points of view of modeling, with 19 currently available databases, and 17 software packages and web servers; fourth, the current state of prediction on parameters in enzymatic reaction in biofuel industry with respect to cellulolytic enzymes were reviewed; fifth, the pros and cons for future development were discussed; and finally, a worked example was given in the Appendix to describe the whole procedures of prediction of enzymatic parameters in reactions.

Keywords

Biofuel Enzyme Prediction Review 

References

  1. 1.
    Bairoch, A. (2000). Nucleic Acids Research, 28, 304–5.CrossRefGoogle Scholar
  2. 2.
    McDonald, A. G., Boyce, S., Moss, G. P., Dixon, H. B., & Tipton, K. F. (2007). BMC Biochemistry, 8, 14.CrossRefGoogle Scholar
  3. 3.
    McDonald, A. G., Boyce, S., & Tipton, K. F. (2009). Nucleic Acids Research, 37, D593–7.CrossRefGoogle Scholar
  4. 4.
    Bannert, C., Welfle, A., Aus-dem Spring, C., & Schomburg, D. (2010). BMC Bioinformatics, 11, 589.CrossRefGoogle Scholar
  5. 5.
    Chen, L. H., Kenyon, G. L., Curtin, F., Harayama, S., Bembenek, M. E., Hajipour, G., & Whitman, C. P. (1992). Journal of Biological Chemistry, 267, 17716–21.Google Scholar
  6. 6.
    Smith, S. (1994). FASEB Journal, 8, 1248–59.Google Scholar
  7. 7.
    Jeong, G. T., & Park, D. H. (2010). Applied Biochemistry and Biotechnology, 161, 195–208.CrossRefGoogle Scholar
  8. 8.
    Samhan-Arias, A. K., Tyurina, Y. Y., & Kagan, V. E. (2011). Journal of Clinical Biochemistry and Nutrition, 48, 91–5.CrossRefGoogle Scholar
  9. 9.
    Ishikawa, Y., & Fujii, S. (2011). Bioinformation, 6, 221–5.CrossRefGoogle Scholar
  10. 10.
    Smith, R. H., Jr., Jorgensen, W. L., Tirado-Rives, J., Lamb, M. L., Janssen, P. A., Michejda, C. J., & Kroeger Smith, M. B. (1998). Journal of Medical Chemistry, 41, 5272–86.CrossRefGoogle Scholar
  11. 11.
    Kumar, V., & Madan, A. K. (2005). European Journal of Pharmaceutical Sciences, 24, 213–8.CrossRefGoogle Scholar
  12. 12.
    Sárváry, E., Nemes, B., Járay, J., Dinya, E., Borka, P., Varga, M., Sulyok, B., Remport, A., Tóth, A., & Perner, F. (2000). Transplantation, 69, 1397–402.CrossRefGoogle Scholar
  13. 13.
    Wang, J. S., Araki, T., Ogawa, T., Sakai, M., Matsuoka, M., & Fukuda, H. (1999). Journal of Theoretical Biology, 196, 9–17.CrossRefGoogle Scholar
  14. 14.
    Kirchmair, J., Williamson, M. J., Tyzack, J. D., Tan, L., Bond, P. J., Bender, A., & Glen, R. C. (2012). Journal of Chemical Information and Modeling, 52, 617–48.CrossRefGoogle Scholar
  15. 15.
    Burgard, P., Rupp, A., Konecki, D. S., Trefz, F. K., Schmidt, H., & Lichter-Konecki, U. (1996). European Journal of Pediatrics, 155(Suppl 1), S11–5.CrossRefGoogle Scholar
  16. 16.
    Berrondo, M., & Gray, J. J. (2011). Proteins, 79, 2844–60.CrossRefGoogle Scholar
  17. 17.
    Chen, W., Feng, P., & Lin, H. (2012). Journal of Industrial Microbiology & Biotechnology, 39, 579–84.CrossRefGoogle Scholar
  18. 18.
    Saremy, S., Boroujeni, M. E., Bhattacharjee, B., Mittal, V., & Chatterjee, J. (2011). Bioinformation, 7, 379–83.CrossRefGoogle Scholar
  19. 19.
    Wu, X. Q., Wang, J., Lü, Z. R., Tang, H. M., Park, D., Oh, S. H., Bhak, J., Shi, L., Park, Y. D., & Zou, F. (2010). Applied Biochemistry and Biotechnology, 160, 1341–55.CrossRefGoogle Scholar
  20. 20.
    Li, J., Schneebeli, S. T., Bylund, J., Farid, R., & Friesner, R. A. (2011). Journal of Chemical Theory and Computation, 7, 3829–45.CrossRefGoogle Scholar
  21. 21.
    Wang, P., Wang, Y., & Su, Z. (2012). Applied Biochemistry and Biotechnology, 167, 62–72.CrossRefGoogle Scholar
  22. 22.
    Moors, S. L., Vos, A. M., Cummings, M. D., Van Vlijmen, H., & Ceulemans, A. (2011). Journal of Medical Chemistry, 54, 6098–105.CrossRefGoogle Scholar
  23. 23.
    Faust, K., & van Helden, J. (2012). Methods in Molecular Biology, 804, 107–30.CrossRefGoogle Scholar
  24. 24.
    Varga, E. G., Titchener-Hooker, N. J., & Dunnill, P. (2001). Biotechnology and Bioengineering, 74, 96–107.CrossRefGoogle Scholar
  25. 25.
    Nicholson, J. K., & Lindon, J. C. (2008). Nature, 455, 1054–6.CrossRefGoogle Scholar
  26. 26.
    Zhang, A., Sun, H., & Wang, X. (2012). Applied Biochemistry and Biotechnology, 168, 1718–27.CrossRefGoogle Scholar
  27. 27.
    Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D. D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J. A., Lim, E., Sobsey, C. A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H. J., & Forsythe, I. (2009). Nucleic Acids Research, 37, D603–10.CrossRefGoogle Scholar
  28. 28.
    OuYang, D., Xu, J., Huang, H., & Chen, Z. (2011). Applied Biochemistry and Biotechnology, 165, 148–54.CrossRefGoogle Scholar
  29. 29.
    Wiggins, J. (2011). Nephron Experimental Nephrology, 119(Suppl 1), e1–5.CrossRefGoogle Scholar
  30. 30.
    Gramer, G., Garbade, S. F., Blau, N., & Lindner, M. (2009). Journal of Inherited Metabolic Disease, 32, 52–7.CrossRefGoogle Scholar
  31. 31.
    Albaek, M. O., Gernaey, K. V., Hansen, M. S., & Stocks, S. M. (2012). Biotechnology and Bioengineering, 109, 950–61.CrossRefGoogle Scholar
  32. 32.
    Armstrong, F. A., & Hirst, J. (2011). Proceedings of National Academy of Sciences of United States of American, 108, 14049–54.CrossRefGoogle Scholar
  33. 33.
    Rothlisberger, U., Carloni, P., Doclo, K., & Parrinello, M. (2000). Journal of Biological Inorganic Chemistry, 5, 236–50.CrossRefGoogle Scholar
  34. 34.
    Michaelis, L., & Menten, M. L. (1913). Biochemische Zeitschrift, 49, 333–69.Google Scholar
  35. 35.
    Price, N. C. (1979). Trends in Biochemical Sciences, 4, pN272.CrossRefGoogle Scholar
  36. 36.
    Cheng, Y., & Prusoff, W. H. (1973). Biochemical Pharmacology, 22, 3099–108.CrossRefGoogle Scholar
  37. 37.
    Ebrahimi, M., Lakizadeh, A., Agha-Golzadeh, P., Ebrahimie, E., & Ebrahimi, M. (2011). PLoS One, 6, e23146.CrossRefGoogle Scholar
  38. 38.
    Barthelmes, J., Ebeling, C., Chang, A., Schomburg, I., & Schomburg, D. (2007). Nucleic Acids Research, 35, D511–4.CrossRefGoogle Scholar
  39. 39.
    Chang, A., Scheer, M., Grote, A., Schomburg, I., & Schomburg, D. (2009). Nucleic Acids Research, 37, D588–92.CrossRefGoogle Scholar
  40. 40.
    Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Söhngen, C., Stelzer, M., Thiele, J., & Schomburg, D. (2011). Nucleic Acids Research, 39, D670–6.CrossRefGoogle Scholar
  41. 41.
    Eadie, G. S. (1942). Journal of Biological Chemistry, 146, 85–93.Google Scholar
  42. 42.
    Hofstee, B. H. J. (1959). Nature, 184, 1296–8.CrossRefGoogle Scholar
  43. 43.
    Hanes, C. S. (1932). Biochemical Journal, 26, 1406–21.Google Scholar
  44. 44.
    Lineweaver, H., & Burk, D. (1934). Journal of the American Chemical Society, 56, 658–66.CrossRefGoogle Scholar
  45. 45.
    Bravo, I. G., Busto, F., De Arriaga, D., Ferrero, M. A., Rodríguez-Aparicio, L. B., Martínez-Blanco, H., & Reglero, A. (2001). Biochemical Journal, 358(Pt 3), 573–83.Google Scholar
  46. 46.
    Biggs, N., Lloyd, E., & Wilson, R. (1986) Graph Theory. Oxford University PressGoogle Scholar
  47. 47.
    King, E. L., & Altman, C. (1956). Journal of Physical Chemistry, 60, 1375–8.CrossRefGoogle Scholar
  48. 48.
    Weber, H., & Richterich, R. (1963). Klinische Wochenschrift, 41, 665–7.CrossRefGoogle Scholar
  49. 49.
    Jenkins, W. T. (1970). Analytical Biochemistry, 38, 409–16.CrossRefGoogle Scholar
  50. 50.
    Katsumata, M. (1972). Journal of Theoretical Biology, 36, 327–38.CrossRefGoogle Scholar
  51. 51.
    Diachina, E. G. (1973). Laboratornoe Delo, 2, 120–1.Google Scholar
  52. 52.
    Ermakov, N. V., & Tokarev, I. N. (1982). Laboratornoe Delo, 10, 17–21.Google Scholar
  53. 53.
    Chou, K. C. (1983). Biophysical Chemistry, 17, 51–5.CrossRefGoogle Scholar
  54. 54.
    Zhou, G. P., & Deng, M. H. (1984). Biochemical Journal, 222, 169–76.Google Scholar
  55. 55.
    Zhao, M. (1992). Biochemical Journal, 287(Pt 2), 391–3.Google Scholar
  56. 56.
    Chou, K. C. (1989). Journal of Biological Chemistry, 264, 12074–9.Google Scholar
  57. 57.
    Lather, V., & Madan, A. K. (2005). Journal of Molecular Graphics and Modelling, 23, 339–45.CrossRefGoogle Scholar
  58. 58.
    Comte, P., Vassiliev, S., Houghten, S., & Bruce, D. (2011). Biosystems, 105, 263–70.CrossRefGoogle Scholar
  59. 59.
    Yuki, H., Honma, T., Hata, M., & Hoshino, T. (2012). Bioorganic and Medicinal Chemistry, 20, 775–83.CrossRefGoogle Scholar
  60. 60.
    Chou, K. C. (2010). Current Drug Metabolism, 11, 369–78.CrossRefGoogle Scholar
  61. 61.
    Chou, K. C., Jiang, S. P., Liu, W. M., & Fee, C. H. (1979). Scientia Sinica, 22, 341–58.Google Scholar
  62. 62.
    Chou, K. C. (1990). Biophysical Chemistry, 35, 1–24.CrossRefGoogle Scholar
  63. 63.
    Wu, G. (1996). Pharmacological Research, 33, 379–83.CrossRefGoogle Scholar
  64. 64.
    el Kebbaj, M. S., & Latruffe, N. (1986). Archives of Biochemistry and Biophysics, 244, 662–70.CrossRefGoogle Scholar
  65. 65.
    Musch, W., Thimpont, J., Vandervelde, D., Verhaeverbeke, I., Berghmans, T., & Decaux, G. (1995). American Journal of Medicine, 99, 348–55.CrossRefGoogle Scholar
  66. 66.
    Prigent, A. (2008). Seminars in Nuclear Medicine, 38, 32–46.CrossRefGoogle Scholar
  67. 67.
    Salgado, J. V., Neves, F. A., Bastos, M. G., França, A. K., Brito, D. J., Santos, E. M., & Salgado Filho, N. (2010). Brazilian Journal of Medical and Biological Research, 43, 528–36.CrossRefGoogle Scholar
  68. 68.
    Gotch, F. A. (1998). Nephrology, Dialysis, Transplantation, 13(Suppl 6), 10–4.CrossRefGoogle Scholar
  69. 69.
    Gotch, F. A., Sargent, J. A., & Keen, M. L. (2000). Kidney International, Suppl 76, S3–S18.CrossRefGoogle Scholar
  70. 70.
    Sigel, R., Sigel, A., & Sigel, H. (2007). The ubiquitous roles of cytochrome P450 proteins: metal ions in life sciences. New York: Wiley.CrossRefGoogle Scholar
  71. 71.
    Mishra, N. K. (2011). Expert Opinion on Drug Metabolism and Toxicology, 7, 1211–31.CrossRefGoogle Scholar
  72. 72.
    Long, W. F., & Labute, P. (2010). Journal of Computer-Aided Molecular Design, 24, 907–16.CrossRefGoogle Scholar
  73. 73.
    Chen, X., Wang, X., Li, Z., Kong, L., Liu, G., Fu, J., & Wang, A. (2012). Gene, 495, 170–7.CrossRefGoogle Scholar
  74. 74.
    Duverle, D. A., & Mamitsuka, H. (2012). Briefings in Bioinformatics, 13, 337–49.CrossRefGoogle Scholar
  75. 75.
    VandenBrink, B. M., Foti, R. S., Rock, D. A., Wienkers, L. C., & Wahlstrom, J. L. (2012). Drug Metabolism and Disposition, 40, 47–53.CrossRefGoogle Scholar
  76. 76.
    Choi, K., & Kim, S. (2011). Journal of Bioinformatics and Computational Biology, 9, 597–611.CrossRefGoogle Scholar
  77. 77.
    Chen, L., Feng, K. Y., Cai, Y. D., Chou, K. C., & Li, H. P. (2010). BMC Bioinformatics, 11, 293.CrossRefGoogle Scholar
  78. 78.
    Basit, N., & Wechsler, H. (2011). Advances in Bioinformatics, 958129.Google Scholar
  79. 79.
    Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2011). Journal of Visualized Experiments, 57, e3259.Google Scholar
  80. 80.
    Needleman, S. B., & Wunsch, C. D. (1970). Journal of Molecular Biology, 48, 443–53.CrossRefGoogle Scholar
  81. 81.
    Wu, G. (2000). Medical Hypotheses, 54, 748–9.CrossRefGoogle Scholar
  82. 82.
    Liu, T., Lin, Y., Wen, X., Jorissen, R. N., & Gilson, M. K. (2007). Nucleic Acids Research, 35, D198–201.CrossRefGoogle Scholar
  83. 83.
    Porter, C. T., Bartlett, G. J., & Thornton, J. M. (2004). Nucleic Acids Research, 32, D129–33.CrossRefGoogle Scholar
  84. 84.
    Bartlett, G. J., Porter, C. T., Borkakoti, N., & Thornton, J. M. (2002). Journal of Molecular Biology, 324, 105–21.CrossRefGoogle Scholar
  85. 85.
    Torrance, J. W., Bartlett, G. J., Porter, C. T., & Thornton, J. M. (2005). Journal of Molecular Biology, 347, 565–81.CrossRefGoogle Scholar
  86. 86.
    Quester, S., & Schomburg, D. (2011). BMC Bioinformatics, 12, 376.CrossRefGoogle Scholar
  87. 87.
    Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012). Nucleic Acids Research, 40, D109–14.CrossRefGoogle Scholar
  88. 88.
    Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., & Hirakawa, M. (2010). Nucleic Acids Research, 38, D355–60.CrossRefGoogle Scholar
  89. 89.
    Holliday, G. L., Andreini, C., Fischer, J. D., Rahman, S. A., Almonacid, D. E., Williams, S. T., & Pearson, W. R. (2012). Nucleic Acids Research, 40, D783–9.CrossRefGoogle Scholar
  90. 90.
    Caspi1, R., Altman, T., Dale, J. M., Dreher, K., Fulcher, C. A., Gilham, F., Kaipa, P., Karthikeyan, A. S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Paley, S., Popescu, L., Pujar, A., Shearer, A. G., Zhang, P., & Karp, P. D. (2010) Nucleic Acids Research, 38 (suppl 1), D473–D479Google Scholar
  91. 91.
    Zhang, P., Foerster, H., Tissier, C. P., Mueller, L., Paley, S., Karp, P. D., & Rhee, S. Y. (2005). Plant Physiology, 138, 27–37.CrossRefGoogle Scholar
  92. 92.
    Caspi, R., Foerster, H., Fulcher, C. A., Hopkinson, R., Ingraham, J., Kaipa, P., Krummenacker, M., Paley, S., Pick, J., Rhee, S. Y., Tissier, C., Zhang, P., & Karp, P. D. (2006). Nucleic Acids Research, 34, D511–6.CrossRefGoogle Scholar
  93. 93.
    Caspi, R., Foerster, H., Fulcher, C. A., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C., Walk, T. C., Zhang, P., & Karp, P. D. (2008). Nucleic Acids Research, 36, D623–31.CrossRefGoogle Scholar
  94. 94.
    Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Pujar, A., Shearer, A. G., Travers, M., Weerasinghe, D., Zhang, P., & Karp, P. D. (2012). Nucleic Acids Research, 40, D742–53.CrossRefGoogle Scholar
  95. 95.
    Lespinet, O., & Labedan, B. (2006). BMC Bioinformatics, 7, 436.CrossRefGoogle Scholar
  96. 96.
    Von Grotthuss, M., Plewczynski, D., Ginalski, K., Rychlewski, L., & Shakhnovich, E. I. (2006). BMC Bioinformatics, 7, 53.CrossRefGoogle Scholar
  97. 97.
    Arcuri, H. A., Zafalon, G. F., Marucci, E. A., Bonalumi, C. E., da Silveira, N. J., Machado, J. M., de Azevedo, W. F., & Jr Palma, M. S. (2010). BMC Bioinformatics, 11, 12.CrossRefGoogle Scholar
  98. 98.
    Hoppe, A., Hoffmann, S., Gerasch, A., Gille, C., & Holzhütter, H. G. (2011). BMC Bioinformatics, 12, 28.CrossRefGoogle Scholar
  99. 99.
    Schremmer, S. D., Waser, M. R., Kohn, M. C., & Garfinkel, D. (1984). Computers and Biomedical Research, 17, 289–301.CrossRefGoogle Scholar
  100. 100.
    Kohn, M. C., Menten, L. E., & Garfinkel, D. (1979). Computers and Biomedical Research, 12, 461–9.CrossRefGoogle Scholar
  101. 101.
    Kohn, M. C., Menten, L. E., & Garfinkel, D. (1981). Computers and Biomedical Research, 14, 91–102.CrossRefGoogle Scholar
  102. 102.
    Damboský, J., Prokop, M., & Koca, J. (2001). Trends in Biochemical Sciences, 26, 71–3.CrossRefGoogle Scholar
  103. 103.
    Prokop, M., Damborský, J., & Koca, J. (2000). Bioinformatics, 16, 845–6.CrossRefGoogle Scholar
  104. 104.
    Prokop, M., Adam, J., Kríz, Z., Wimmerová, M., & Koca, J. (2008). Bioinformatics, 24, 1955–6.CrossRefGoogle Scholar
  105. 105.
    Schwarz, R., Musch, P., von Kamp, A., Engels, B., Schirmer, H., Schuster, S., & Dandekar, T. (2005). BMC Bioinformatics, 6, 135.CrossRefGoogle Scholar
  106. 106.
    Otto, T. D., Guimarães, A. C., Degrave, W. M., & de Miranda, A. B. (2008). BMC Bioinformatics, 9, 544.CrossRefGoogle Scholar
  107. 107.
    Latendresse, M., & Karp, P. D. (2011). BMC Bioinformatics, 12, 176.CrossRefGoogle Scholar
  108. 108.
    Li, G. H., & Huang, J. F. (2010). BMC Bioinformatics, 11, 439.CrossRefGoogle Scholar
  109. 109.
    Audit, B., Levy, E. D., Gilks, W. R., Goldovsky, L., & Ouzounis, C. A. (2007). BMC Bioinformatics, 8(Suppl 4), S3.CrossRefGoogle Scholar
  110. 110.
    Hung, S. S., Wasmuth, J., Sanford, C., & Parkinson, J. (2010). Bioinformatics, 26, 1690–8.CrossRefGoogle Scholar
  111. 111.
    Arakaki, A. K., Huang, Y., & Skolnick, J. (2009). BMC Bioinformatics, 10, 107.CrossRefGoogle Scholar
  112. 112.
    Bevc, S., Konc, J., Stojan, J., Hodošček, M., Penca, M., Praprotnik, M., & Janežič, D. (2011). PLoS One, 6, e22265.CrossRefGoogle Scholar
  113. 113.
    Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., & Kanehisa, M. (2009). Bioinformatics, 25, i179–86.CrossRefGoogle Scholar
  114. 114.
    Shen, H. B., & Chou, K. C. (2007). Biochemical and Biophysical Research Communications, 364, 53–9.CrossRefGoogle Scholar
  115. 115.
    Li, C., Li, Y., Zhang, X., Stafford, P., & Dinu, V. (2009). BMC Bioinformatics, 10, 286.CrossRefGoogle Scholar
  116. 116.
    Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., & Kanehisa, M. (2010). Nucleic Acids Research, 38, W138–43.CrossRefGoogle Scholar
  117. 117.
    Zhang, K., Xu, Y., & Chen, G. (2008). International Journal of Bioinformatics Research and Applications, 4, 295–305.CrossRefGoogle Scholar
  118. 118.
    Yan, S., Shi, D., Nong, H., & Wu, G. (2011). Guangxi Sciences, 18, 253–60.Google Scholar
  119. 119.
    Yan, S., & Wu, G. (2011). Applied Biochemistry and Biotechnology, 165, 856–69.CrossRefGoogle Scholar
  120. 120.
    Yan, S., & Wu, G. (2012). Applied Biochemistry and Biotechnology, 166, 997–1107.CrossRefGoogle Scholar
  121. 121.
    Yan, S. M., & Wu, G. (2011). Protein Peptide Letters, 18, 1053–7.CrossRefGoogle Scholar
  122. 122.
    Yan, S., & Wu, G. (2012). Protein Peptide Letters, 19, 29–39.CrossRefGoogle Scholar
  123. 123.
    Yan, S., Shi, D., Nong, H., & Wu, G. (2012). Interdisciplinary Science Computational Life Sciences, 4, 46–53.CrossRefGoogle Scholar
  124. 124.
    Yan, S., & Wu, G. (2011). Enzyme Engineering, 1, 102.Google Scholar
  125. 125.
    Yan, S., & Wu, G. (2012). Protein Peptide Letters, 20, 255–64.Google Scholar
  126. 126.
    Carroll, A., & Somerville, C. (2009). Annual Review of Plant Biology, 60, 165–82.CrossRefGoogle Scholar
  127. 127.
    Barnard, D., Casanueva, A., Tuffin, M., & Cowan, D. (2010). Environmental Technology, 31, 871–88.CrossRefGoogle Scholar
  128. 128.
    van Zyl, W. H., Bloom, M., & Viktor, M. J. (2012). Applied Microbiology and Biotechnology, 95, 1377–88.CrossRefGoogle Scholar
  129. 129.
    Fuciños, P., González, R., Atanes, E., Sestelo, A. B., Pérez-Guerra, N., Pastrana, L., & Rúa, M. L. (2012). Methods in Molecule Biology, 861, 239–66.CrossRefGoogle Scholar
  130. 130.
    Duan, C. J., & Feng, J. X. (2010). Biotechnology Letters, 32, 1765–75.CrossRefGoogle Scholar
  131. 131.
    Yu, E. H., Prodanovic, R., Güven, G., Ostafe, R., & Schwaneberg, U. (2011). Applied Biochemistry and Biotechnology, 165, 1448–57.CrossRefGoogle Scholar
  132. 132.
    Nghiem, N. P., Taylor, F., Johnston, D. B., Shetty, J. K., & Hicks, K. B. (2011). Applied Biochemistry and Biotechnology, 165, 870–82.CrossRefGoogle Scholar
  133. 133.
    Ribeiro, B. D., de Castro, A. M., Coelho, M. A., & Freire, D. M. (2011). Enzyme Research, 2011, 615803.Google Scholar
  134. 134.
    Struck, A. W., Thompson, M. L., Wong, L. S., & Micklefield, J. (2012). Chembiochem, 13, 2642–55.CrossRefGoogle Scholar
  135. 135.
    Jeong, Y. S., Na, H. B., Kim, S. K., Kim, Y. H., Kwon, E. J., Kim, J., Yun, H. D., Lee, J. K., & Kim, H. (2012). Applied Biochemistry and Biotechnology, 166, 1328–39.CrossRefGoogle Scholar
  136. 136.
    Sheldon, R. A. (2011). Applied Microbiology and Biotechnology, 92, 467–77.CrossRefGoogle Scholar
  137. 137.
    Skoko, N., Baralle, M., Tisminetzky, S., & Buratti, E. (2011). Molecular Biotechnology, 48, 290–7.CrossRefGoogle Scholar
  138. 138.
    Li, Q., Zhao, Q., Hu, Y., & Wang, H. (2006). Biotechnological Journal, 1, 1205–14.Google Scholar
  139. 139.
    Ibrahim, C. O. (2008). Bioresource Technology, 99, 4572–82.CrossRefGoogle Scholar
  140. 140.
    de Castro, A. M., Carvalho, D. F., Freire, D. M., & Dos Reis Castilho, L. (2010). Enzyme Research, 2010, 576872.Google Scholar
  141. 141.
    Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., & Kanehisa, M. (2008). Nucleic Acids Research, 36, D202–5.CrossRefGoogle Scholar
  142. 142.
    Wu, G., & Yan, S. (2008). Lecture notes on computational mutation. New York: Nova Science.Google Scholar
  143. 143.
    Yang, X. Y., Shi, X. H., Meng, X., Li, X. L., Lin, K., Qian, Z. L., Feng, K. Y., Kong, X. Y., & Cai, Y. D. (2010). Protein Peptide Letters, 17, 899–908.CrossRefGoogle Scholar
  144. 144.
    Atchley, W. R., Zhao, J., Fernandes, A. D., & Druke, T. (2005). Proceedings of National Academy of Sciences of United States of American, 102, 6395–400.CrossRefGoogle Scholar
  145. 145.
    Zamyatin, A. A. (1972). Progress in Biophysics and Molecular Biology, 24, 107–23.CrossRefGoogle Scholar
  146. 146.
    Darby, N. J., & Creighton, T. E. (1993). Journal of Molecular Biology, 232, 873–96.CrossRefGoogle Scholar
  147. 147.
    Kyte, J., & Doolittle, R. F. (1982). Journal of Molecular Biology, 157, 105–32.CrossRefGoogle Scholar
  148. 148.
    Trinquier, G., Sanejouand, Y. H., & Hausman, R. E. (1998). Protein Engineering, 11, 153–69.CrossRefGoogle Scholar
  149. 149.
    Cooper, G. M. (2004). The cell: a molecular approach (p. 51). Washington, D.C: ASM.Google Scholar
  150. 150.
    Dwyer, D. S. (2005). BMC Chemical Biology, 5, 2.CrossRefGoogle Scholar
  151. 151.
    Chou, P. Y., & Fasman, G. D. (1978). Advances in Enzymology and Related Subjects of Biochemistry, 47, 45–148.Google Scholar
  152. 152.
    Burlingame, A. L., & Carr, S. A. (1996). Mass spectrometry in the biological sciences. Totowa, NJ: Humana.CrossRefGoogle Scholar
  153. 153.
    Hagan, M. T., Demuth, H. B., & Beale, M. H. (1996). Neural network design. Boston, MA: PWS.Google Scholar
  154. 154.
    Demuth, H., & Beale, M. (2001) Neural Network Toolbox for Use with MatLab. User’s guide, version 4.Google Scholar
  155. 155.
    MathWorks Inc. (2001) MatLab—the language of technical computing (version 6.1.0.450, release 12.1), 1984–2001.Google Scholar
  156. 156.
    Chou, K. C. (2011). Journal of Theoretical Biology, 273, 236–47.CrossRefGoogle Scholar
  157. 157.
    Chou, K. C., & Shen, H. B. (2007). Analytical Biochemistry, 370, 1–16.CrossRefGoogle Scholar
  158. 158.
    Chou, K. C., & Shen, H. B. (2010). PLoS One, 5, e9931.CrossRefGoogle Scholar
  159. 159.
    Wu, G., Baraldo, M., & Furlanut, M. (1995). Pharmacological Research, 32, 241–8.CrossRefGoogle Scholar
  160. 160.
    Wu, G. (1995). Pharmacological Research, 31, 393–9.CrossRefGoogle Scholar
  161. 161.
    Zhou, W., Irwin, D. C., Escovar-Kousen, J., & Wilson, D. B. (2004). Biochemistry, 43, 9655–63.CrossRefGoogle Scholar
  162. 162.
    Kang, H. J., & Ishikawa, K. (2007). Journal of Microbiology and Biotechnology, 17, 1249–53.Google Scholar
  163. 163.
    Kim, H. W., Takagi, Y., Hagihara, Y., & Ishikawa, K. (2007). Bioscience, Biotechnology and Biochemistry, 71, 2585–7.CrossRefGoogle Scholar
  164. 164.
    The UniProt Consortium. (2010) Nucleic Acids Research, 38, D142–D148.Google Scholar
  165. 165.
    Akaike, H. (1974). IEEE Transactions on Automatic Control, 19, 716–23.CrossRefGoogle Scholar
  166. 166.
    Feller, W. (1968). An introduction to probability theory and its applications. 3rd ed. Vol, I. New York: Wiley.Google Scholar
  167. 167.

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food BiorefineryGuangxi Key Laboratory of Biorefinery, Guangxi Academy of SciencesNanningChina

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