An Intriguing Controversy over Protein Structural Class Prediction (original) (raw)

REFERENCES

• Bahar, I., Atilgan, A. R., Jernigan, R. L., and Erman, B. (1997). Understanding the recognition of protein structural classes by amino acid composition, Proteins 29, 172–185.
  Article CAS PubMed Google Scholar
• Chandonia, J. M., and Karplus, M. (1995). Neural networks for secondary structure and structural class prediction, Protein Sci. 4, 275–285.
  Article CAS PubMed PubMed Central Google Scholar
• Chou, K. C. (1995). A novel approach to predicting protein structural classes in a (20 -- 1)-D amino acid composition space, Proteins Struct. Funct. Genet. 21, 319–344.
  Article CAS PubMed Google Scholar
• Chou, K. C., and Zhang, C. T. (1995). Prediction of protein structural classes, Crit. Rev. Biochem. Mole. Biol. 30, 275–349.
  Article CAS Google Scholar
• Chou, P. Y. (1980). Amino acid composition of four classes of proteins, In Abstracts of Papers, Part I, Second Chemical Congress of the North American Continent, Las Vegas, Nevada.
• Chou, P. Y. (1989). Prediction of protein structural classes from amino acid composition, In Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum Press, New York, pp. 549–586.
  Chapter Google Scholar
• Dubchak, I., Holbrook, S. R., and Kim, S.-H. (1993). Predicting protein secondary structure content: A tandem neural network approach, Proteins Struct. Funct. Genet. 16, 79–91.
  Article CAS PubMed Google Scholar
• Duda, R. O., and Hart, P. E. (1973). Pattern Classification and Scene Analysis, Wiley, New York, Chapter 2.
  Google Scholar
• Eisenhaber, F., Frömmel, C., and Argos, P. (1996). Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class, Proteins Struct. Funct. Genet. 25, 169–179.
  Article CAS PubMed Google Scholar
• Farber, G. K., and Petsko, G. A. (1990). The evolution of α/β barrel enzymes, TIBS 15, 228–234.
  CAS PubMed Google Scholar
• Kabsch, W., Mannherz, H. G., Suck, D., Pai, E. F., and Holms, K. C. (1990). Atomic structure of the actin:DNase 1 complex, Nature 347, 37–44.
  Article CAS PubMed Google Scholar
• Kabsch, W., and Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577–2637.
  Article CAS PubMed Google Scholar
• Klein, P., and Delisi, C. (1986). Prediction of protein structural class from amino acid sequence, Biopolymers 25, 1659–1672.
  Article CAS PubMed Google Scholar
• Levitt, M., and Chothia, C. (1976). Structural patterns in globular proteins, Nature 261, 552–557.
  Article CAS PubMed Google Scholar
• Mahalanobis, P. C. (1936). On the generalized distance in statistics, Proc. Natl. Inst. Sci. India 2, 49–55.
  Google Scholar
• Mardia, K. V., Kent, J. T., and Bibby, J. M. (1979) Multivariate Analysis. Academic Press, London, pp. 322 and 381.
  Google Scholar
• Metfessel, B. A., Saurugger, P. N., Connelly, D. P., and Rich, S. T. (1993). Cross-validation of protein structural class prediction using statistical clustering and neural networks, Protein Sci. 2, 1171–1182.
  Article CAS PubMed PubMed Central Google Scholar
• Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995). SCOP: A structural classification of protein database for the investigation of sequence and structures, J. Mol. Biol. 247, 536–540.
  Article CAS PubMed Google Scholar
• Muskal, S. M., and Kim, S.-H. (1992). Predicting protein secondary structure content: A tandem neural network approach, J. Mol. Biol. 225, 713–727.
  Article CAS PubMed Google Scholar
• Nakashima, H., Nishikawa, K., and Ooi, T. (1986). The folding type of a protein is relevant to the amino acid composition, J. Biochem. 99, 152–162.
  Article Google Scholar
• Pillai, K. C. S. (1985). Mahalanobis D 2, In Encyclopedia of Statistical Sciences (Kotz, S., and Johnson, N. L., eds.), Wiley, New York, Vol. 5, pp. 176–181.
  Google Scholar
• Rost, B., and Sander, C. (1994). Combining evolutionary information and neural networks to predict protein secondary structure, Protein Struct. Funct. Genet. 19, 55–72.
  Article CAS Google Scholar
• Sondek, J., and Shortle, D. (1990). Accomodation of single amino acid insertions by the native state of staphyloccocal nuclease, Proteins Struct. Funct. Genet. 7, 299–305.
  Article CAS PubMed Google Scholar
• Zhang, C. T., and Chou, K. C. (1992). An optimization approach to predicting protein structural class from amino acid composition, Protein Sci. 1, 401–408.
  Article CAS PubMed PubMed Central Google Scholar

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