Abstract
In the absence of crystallographic data, many structural features of proteins can be deduced from the analysis of protein sequences. One of the most promising tools for the near future relates to the prediction of antigenic sites (for a review, see Berzofsky, 1985; Delisi and Berzofsky, 1985; Margalit et al., 1987) for the engineering of synthetic vaccines. In addition, with the increasing number of protein sequences known from DNA cloning and sequencing, the need for a theoretical treatment of protein sequences has never been greater. In this context, many different methods for predicting the secondary structure of proteins have been developed (Finkelstein and Ptitsyn, 1971; Robson and Pain, 1971; Kabat and Wu, 1973; Burgess et al., Chou and Fasman, 1974; Lim, 1974; Nagano, 1977; Garnier et al., 1978; Cid et al., 1982). Several of these methods are statistical i.e., they are based on the observed frequency with which individual residues are found in given structural states.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Berzofsky, J. A., 1985, Intrinsic and extrinsic factors in protein antigenic structure, Science 229:932–940.
Burgess, A. W., Ponnuswamy, P. K., and Scheraga, H. A., 1974, Analysis of conformations of amino acid residues and prediction of backbone topography in proteins, Isr. J. Chem. 12:239–286.
Busetta, B., 1986, Examination of folding patterns for predicting protein topologies, Biochim. Biophys. Acta 870:327–338.
Busetta, B., and Barrans, Y., 1984, The prediction of protein domains, Biochim. Biophys. Acta 790: 117–124.
Chou, P. Y., and Fasman, G. D., 1974, Prediction of protein conformation, Biochemistry 13:222–244.
Chou, P. Y., and Fasman, G. D., 1978, Prediction of secondary structure of proteins from amino acid sequence, Adv. Enzymol. Relat. Subj. Biochem. 47:45–148.
Cid, H., Bunster, M., Arriagada, E., and Campos, M., 1982, Prediction of secondary structure of proteins by means of hydrophobicity profiles, FEBS Lett. 150:247–254.
Corrigan, A. J., and Huang, P. C., 1982, A BASIC microcomputer program for plotting the secondary structure of proteins, Comput. Prog. Biomed. 15:163–168.
Deléage, G., and Roux, B., 1987, An algorithm for protein secondary structure prediction based on class prediction, Protein Eng. 1:289–294.
Deléage, G., Tinland, B., and Roux, B., 1987, A computerized version of the Chou and Fasman method for predicting the secondary structure of proteins, Anal. Biochem. 163:292–297.
Deléage, G., Clerc, F. F., Roux, B., and Gautheron, D. C., 1988, ANTHEPROT: A package for protein sequence analysis using a microcomputer, CABIOS 4:351–356.
Delisi, C., and Berzofsky, J. A., 1985, T-cell antigenic sites tend to be amphipathic structures, Proc. Natl. Acad. Sci. U.S.A. 82:7048–7052.
Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1982, The helical hydrophobic moment: A measure of the amphiphilicity of a helix, Nature 299:371–374.
Finkelstein, A. V., and Ptitsyn, O. B., 1971, Statistical analysis of the correlation among amino acid residues in helical, ß-structural and non-regular regions of globular proteins, J. Mol. Biol. 62:613–624.
Garatt, R. C., Taylor, W. R., and Thornton, J. M., 1985, The influence of tertiary structure on secondary structure prediction, FEBS Lett. 188:59–62.
Garnier, J., Osguthorpe, D. J., and Robson, B., 1978, Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J. Mol. Biol. 120:97–120.
Kabat, E. A., and Wu, T. T., 1973, The influence of nearest-neighbor amino acids on the conformation of the middle amino acid in proteins: Comparison of predicted and experimental determination of ß sheets in concanavalin A, Proc. Natl. Acad. Sci. U.S.A. 70:1473–1477.
Kabsch, W., and Sander, C., 1983a, How good are predictions of protein secondary structure? FEBS Lett. 155: 179–182.
Kabsch, W., and Sander, C., 1983b, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22:2577–2637.
Klein, P., and Delisi, C., 1986, Prediction of protein structural class from the amino acid sequence, Biopolymers 25:1659–1672.
Levin, J. M., Robson, B., and Garnier, J., 1986, An algorithm for secondary structure determination in proteins based on sequence similarity, FEBS Lett. 205:303–308.
Levitt, M., and Chothia, C., 1976, Structural patterns in globular proteins, Nature 261:552–558.
Lim, V. I., 1974, Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure, J. Mol. Biol. 88:857–872.
Margalit, H., Spouge, J. L., Cornette, J. L., Cease, K. P., Delisi, C., and Berzofsky, J. A., 1987, Prediction of immunodominant helper T cell antigenic sites from the primary sequence, J. Immunol. 138:2213–2229.
Nagano, K., 1977, Triplet information in helix prediction applied to the analysis of super-secondary structures, J. Mol. Biol. 109:251–274.
Nakashima, H., Nishikawa, K., and Ooi, T., 1986, The folding type of a protein is relevant to the amino acid composition, J. Biochem. (Tokyo) 99:153–162.
Nishikawa, K., 1983, Assessment of secondary-structure prediction of proteins. Comparison of computerized Chou-Fasman method with others, Biochim. Biophys. Acta 748:285–299.
Nishikawa, K., and Ooi, T., 1986, Amino acid sequence homology applied to the prediction of protein secondary structure, and joint prediction with existing methods, Biochim. Biophys. Acta 871:45–54.
Parilla, A., Domenech, A., and Querol, E., 1986, A pascal microcomputer program for prediction of protein secondary structure and hydropathic segments, Cabios 2:211–215.
Ralph, W. W., Webster, T., and Smith, T. F., 1987, A modified Chou and Fasman protein structure algorithm, Cabois 3:211–216.
Rawlings, N., Ashman, K., and Wittmann-Liebold, B., 1983, Computerized version of the Chou and Fasman protein secondary structure predictive method, Int. J. Peptide Res. 22:515–524.
Richardson, J. S., 1981, The anatomy and taxonomy of protein structure, Adv. Prot. Chem. 34:167–339.
Robson, B., and Pain, R. H., 1971, Analysis of the code relating sequence to conformation in proteins: Possible implications for the mechanism of formation of helical regions, J. Mol. Biol. 58:237–259.
Sweet, R. M., 1986, Evolutionary similarity among peptide segments is a basis for prediction of protein folding, Biopolymers 25: 1565–1577.
Taylor, W. R., and Thornton, J. M., 1983, Prediction of super-secondary structure in proteins, Nature 301: 540–542.
Vonderviszt, F., and Simon, I., 1986, A possible way for prediction of domain boundaries in globular proteins from amino acid sequence, Biochem. Biophys. Res. Commun. 139:11–17.
Zvelebil, M. J., Barton, G. J., Taylor, W. R., and Sternberg, M. J. E., 1987, Prediction of protein secondary structure and active sites using the alignment of homologous sequences, J. Mol. Biol. 195:957–961.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1989 Plenum Press, New York
About this chapter
Cite this chapter
Deléage, G., Roux, B. (1989). Use of Class Prediction to Improve Protein Secondary Structure Prediction. In: Fasman, G.D. (eds) Prediction of Protein Structure and the Principles of Protein Conformation. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-1571-1_13
Download citation
DOI: https://doi.org/10.1007/978-1-4613-1571-1_13
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4612-8860-2
Online ISBN: 978-1-4613-1571-1
eBook Packages: Springer Book Archive