The GOR Method for Predicting Secondary Structures in Proteins

  • J. Garnier
  • B. Robson


The widely used term “secondary structure” implies that it is of value to consider the structure of a protein as organized hierarchically. “Hierarchic” relates to the idea that the structure can be considered on at least two levels; there are, in fact, three levels of interest here, namely, the covalent structure (primary), the structural organization of stereoregular regions as specific backbone conformations (secondary), and the way in which they are assembled in a three-dimensional conformation (tertiary structure) to make a protein. The recently introduced concept of “supersecondary” structure intermediate to secondary and tertiary levels describes the interactions between secondary structures in space. It should also be stated that the more recently recommended definition of secondary structure covers all backbone conformations, stereoirregular as well as stereoregular.


Secondary Structure Amino Acid Residue Data Base Globular Protein Conformational State 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977, The protein data bank: A computer-based archival file for macromolecular structures, J. Mol. Biol. 112:535–543.PubMedCrossRefGoogle Scholar
  2. Biou, V., Gibrat, J. F., Levin, J., Robson, B., and Garnier, J., 1988, Secondary structure prediction: Combination of three different methods, Protein Engineering 2:185–191.PubMedCrossRefGoogle Scholar
  3. Brillouin, L., 1956, Science and Information Theory, Academic Press, New York.Google Scholar
  4. Busetta, B., and Hospital, M., 1982, An analysis of the prediction of secondary structures, Biochim. Biophys. Acta 701:111–118.CrossRefGoogle Scholar
  5. Chou, P. Y., and Fasman, G. D., 1974, Prediction of protein conformation, Biochemistry 13:222–245.PubMedCrossRefGoogle Scholar
  6. Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J., 1986, Turn prediction in proteins using a pattern matching approach, Biochemistry 25:266–275.PubMedCrossRefGoogle Scholar
  7. Fano, R., 1961, Transmission of Information, John Wiley & Sons, New York.Google Scholar
  8. Fisher, R. A., 1934, Statistical Methods for Research Workers, Oliver and Boyd, London, pp. 99–101.Google Scholar
  9. Garnier, J., and Robson, B., 1979, Classes of protein folding and accuracy of prediction, in: Workshop on Protein Structure, CECAM, Orsay, France, pp. 147–148.Google Scholar
  10. Garnier, J., Salesse, R., Rerat, B., Rerat, C., and Blake, C., 1976, Comparison of x-ray data to estimated secondary structures from amino acid sequence and circular dichroism of human prealbumin, J. Chimie Phys. 73:1019–1023.Google Scholar
  11. Garnier, J., Osguthorpe, D. J., and Robson, B., 1978, Analysis of the accuracy and implications of simple method for predicting the secondary structure of globular proteins, J. Mol. Biol. 120:97–120.PubMedCrossRefGoogle Scholar
  12. Gibrat, J. F., 1986, Modelisation by Computers of the 3-D Structure of Proteins, Ph.D. thesis, University of Paris VI, Paris.Google Scholar
  13. Gibrat, J. F., Gamier, J., and Robson, B., 1987, Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs, J. Mol. Biol. 198:425–443.PubMedCrossRefGoogle Scholar
  14. Kabsch, W., and Sander, C., 1983a, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22:2577–2637.PubMedCrossRefGoogle Scholar
  15. Kabsch, W., and Sander, C., 1983b, How good are predictions of protein secondary structure? FEBS Lett. 155: 179–182.PubMedCrossRefGoogle Scholar
  16. Lee, B., and Richards, F. M., 1971, The interpretation of protein structures: Estimation of static accessibility, J. Mol. Biol. 55:379–400.PubMedCrossRefGoogle Scholar
  17. Levin, J. M., and Garnier, J., 1988, Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool, Biochim. Biophys. Acta. 955:283–295.PubMedCrossRefGoogle Scholar
  18. 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.PubMedCrossRefGoogle Scholar
  19. Levitt, M., and Greer, J., 1977, Automatic identification of secondary structure in globular proteins, J. Mol. Biol. 114:181–293.PubMedCrossRefGoogle Scholar
  20. Lim, V. I., 1974, Algorithm for prediction of α-helical and ß-structural regions in globular proteins, J. Mol. Biol. 88:873–894.PubMedCrossRefGoogle Scholar
  21. Matthews, B. B., 1975, Comparison of the predicted and observed secondary structure of T4 phage lysozyme, Biochim. Biophys. Acta 405:442–451.PubMedGoogle Scholar
  22. Maxfield, F. R., and Scheraga, H. A., 1975, The effect of neighboring charges on the helix forming ability of charged amino acids in proteins, Macromolecules 8:491–493.PubMedCrossRefGoogle Scholar
  23. Maxfield, F. R., and Scheraga, H. A., 1976, Status of empirical methods for the prediction of protein backbone topography, Biochemistry 15:5138–5153.PubMedCrossRefGoogle Scholar
  24. Nakashima, H., Nishikawa, K., and Ooi, T., 1986, The folding type of a protein is relevant to the amino acid composition, J. Biochem. 99:153–162.PubMedGoogle Scholar
  25. Pain, R. H., and Robson, B., 1970, Analysis of the code relating sequence to secondary structure in proteins, Nature 227:62–63.PubMedCrossRefGoogle Scholar
  26. Richardson, J. S., 1981, The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34:167–339.PubMedCrossRefGoogle Scholar
  27. Robson, B., 1974, Analysis of the code relating sequence to conformation in globular proteins, Biochem. J. 141:853–867.PubMedGoogle Scholar
  28. Robson, B., and Garnier, J., 1986, Introduction to Proteins and Protein Engineering, Elsevier, Amsterdam.Google Scholar
  29. 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.PubMedCrossRefGoogle Scholar
  30. Robson, B., and Suzuki, E., 1976, Conformational properties of amino acids residues in globular proteins, J. Mol. Biol. 107:327–356.PubMedCrossRefGoogle Scholar
  31. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H., 1985, Hydrophobicity of amino acid residues in globular proteins, Science 229:834–838.PubMedCrossRefGoogle Scholar
  32. Schiffer, M., and Edmundson, A. B., 1967, Use of helical wheels to represent the structures of protein and to identify segments with helical potential, Biophys. J. 7:121–135.PubMedCrossRefGoogle Scholar
  33. Schwartz, R. M., and Dayhoff, M. O., 1978, Matrices for detecting distant relationships in: Atlas of Protein Sequence and Structure, Volume 5, Suppl. 3 (M. O. Dayhoff, ed.), National Biochemical Research Foundation, Washington, pp. 353–358.Google Scholar
  34. Taylor, W. R., and Thornton, J. M., 1983, Prediction of supersecondary structure in proteins, Nature 301:540–542.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • J. Garnier
    • 1
  • B. Robson
    • 2
    • 3
  1. 1.Laboratory of Physical BiochemistryUniversity of Paris-SudOrsayFrance
  2. 2.Proteus Biotechnology Ltd.Marple, CheshireEngland
  3. 3.Epistron Peptide and Protein Engineering Research UnitUniversity of ManchesterManchesterEngland

Personalised recommendations