Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class

Proteins: Structure, Function and Genetics

Volumn 25, Issue 2, 1996, Pages 169-179

  Eisenhaber, Frank ^a,b   Frömmel, Cornelius ^a   Argos, Patrick ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

amino acid composition; jackknife analysis; prediction of folding type; prediction of secondary structural class; protein structure prediction

Indexed keywords

AMINO ACID COMPOSITION; ARTICLE; COMPUTER ANALYSIS; CONFORMATIONAL TRANSITION; DATA BASE; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0029902174     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199606)25:2<169::AID-PROT3>3.3.CO;2-5     Document Type: Article

References (35)

1. Nishikawa, K., Ooi, T. Correlation of the amino acid composition of a protein to its structural and biological characters. J. Biochem. 91:1821-1824, 1982.
2. Nishikawa, K., Kubota, Y., Ooi, T. Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types. J. Biochem. 94:997-1007, 1983.
3. Sheridan, R.P., Dixon, J.S., Venkataraghavan, R., Kuntz, I.D., Scott, K.P. Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures. Biopolymers 24:1995-2023, 1985.
4. Nakashima, H., Nishikawa, K., Ooi, T. The folding type of a protein is relevant to the amino acid composition. J. Biochem. 99:153-162, 1986.
5. Chou PY; Prediction of protein structural classes from amino acid composition. In: Prediction of Protein Structure." Fasman, G.D. (ed.). New York: Plenum Press, 1989: 549-586.
6. Zhang, C.-T., Chou, K.-C. An optimization approach to predicting protein structural class from amino acid composition. Protein Sci. 1:401-408, 1992.
7. Chou, K.-C., Zhang, C.-T. A correlation-coefficient method to predicting protein-structural classes from amino acid composition. Eur. J. Biochem. 207:429-433, 1992.
8. Zhou, G., Xu, X., Zhang, C.-T. A weighting method for prediction of protein structural class from amino acid composition. Eur. J. Biochem. 210:747-749, 1992.
9. Chou, K.-C., Zhang, C.-T. A new approach to prediction protein folding types. J. Prot. Chem. 12:169-178, 1993.
10. Mao, B., Chou, K.-C., Zhang, C.-T. Protein folding classes: A geometric interpretation of the amino acid composition of globular proteins. Protein Eng. 7:319-330, 1994.
11. Chou, K.-C., Zhang, C.-T. Predicting folding types by distance functions that make allowance for amino acid interactions. J. Biol. Chem. 269:22014-22020, 1994.
12. Chou, K.-C. Does the folding type depend on its amino acid composition? FEBS Lett. 363:127-131, 1995.
13. Chou, K.-C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21:319-344, 1995.
14. Zhang, C.-T., Chou, K.-C. An eigenvalue-eigenvector approach to predicting protein folding types. J. Prot. Chem. 14:309-326, 1995.
15. Chou, K.-C., Zhang, C.-T. Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995.
16. Metfessel, B.A., Saurugger, P.N., Connelly, D.P., Rich, S.S. Cross-validation of protein structural class prediction using statistical clustering and neural networks. Protein Sci. 2:1171-1182, 1993.
17. Reczko, M., Cohr, H., Subramaniam, S., Pamigighantam, S., Hatzigeorgiou, A. Fold-class prediction by neural networks. In: "Protein Structure by Distance Analysis." Bohr, H., Brunak, S. (eds.). Amsterdam, Tokyo: IOS Press, Ohmsha, 1994:277-286.
18. Reczko, M., Bohr, H. The DEF data base of sequence based protein fold class predictions. Nucleic Acids Res. 22:3616-3619, 1994.
19. Chandonia, J.-M., Karplus, M. Neural networks for secondary structure and structural class predictions. Protein Sci. 4:275-285, 1995.
20. Rost, B., Sander, C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232:584-599, 1993.
21. Levin, J.M., Pascarella, S., Argos, P., Garnier, J. Quantification of secondary structure prediction improvement using multiple alignments. Protein Eng. 6:849-854, 1993.
22. Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72, 1994.
23. Eisenhaber, F., Persson, B., Argos, P. Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol. 30:1-94, 1995.
24. Barton, G.J. Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5:372-376, 1995.
25. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. Protein data bank: A computer based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
26. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. "Protein Data Bank, Crystallographic Data-bases - Information Content, Software Systems, Scientific Applications." Allen, F.H., Bergerhoff, G., Sievers, R., (eds.). Bonn/Cambridge/Chester: Data Commission of the International Union of Crystallography, 1987:107-132.
27. Heringa, J., Sommerfeldt, H., Higgins, D., Argos, P. OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput. Appl. Biosci. 8:599-600, 1992.
28. Schrauber, H., Eisenhaber, F., Argos, P., Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J. Mol. Biol. 230:592-612, 1993.
29. Kabsch, W., Sander, C. Dictionary of protein secondary structures: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
30. Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B., Mornon, J.-P. Comparison of three algorithms for the assignment of secondary structure in proteins: The advantage of a consensus assignment. Protein Eng. 6:377-382, 1993.
31. Levitt, M., Chothia, C. Structural patterns in globular proteins. Nature 261:552-558, 1976.
32. Klein, P., DeLisi, C. Prediction of protein structural class from the amino acid sequence. Biopolymers 25:1659-1672, 1986.
33. Boberg, J., Salakoski, T., Vihinen, M. Accurate prediction of protein secondary structural class with fuzzy structural vectors. Protein. Eng. 8:505-512, 1995.
34. Zhang, C.-T., Chou, K.-C., Maggiora, G.M. Predicting protein structural class from amino acid composition: Application of fuzzy clustering. Protein Eng. 8:425-435, 1995.
35. Kneller, D.G., Cohen, F.E., Langridge, R. Improvements in secondary structure prediction by enhanced neural networks. J. Mol. Biol. 214:171-182.