Understanding the recognition of protein structural classes by amino acid composition

Proteins: Structure, Function and Genetics

Volumn 29, Issue 2, 1997, Pages 172-185

  Bahar, Ivet ^a,b   Atilgan, Ali Rana ^b   Jernigan, Robert L ^a   Erman, Burak ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Contact patterns; Coordination of amino acids; Kirchhoff matrices; Lattice models; Non bonded contacts; Secondary structure content prediction; Singular value decomposition

Indexed keywords

AMINO ACID ANALYSIS; ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THERMODYNAMICS;

AMINO ACIDS; PROTEIN CONFORMATION; PROTEINS;

EID: 0030955263     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199710)29:2<172::AID-PROT5>3.0.CO;2-F     Document Type: Article

References (33)

1. Zhang, C.T., Chou, K.C. An optimization approach to predicting protein structural class from amino acid composition. Protein Sci. 1:401-408, 1992.
2. Dubchak, I., Holbrook, S.R., Kim, S.H. Prediction of protein folding class from amino acid composition. Proteins 16:79-91, 1993.
3. Chou, K.C. Does the folding type of a protein depend on its amino acid composition? FEBS Lett. 363:127-131, 1995.
4. Zhang, C.T., Chou, K.C., Maggiora, G.M. Predicting protein structural classes from amino acid composition: Application of fuzzy clustering. Protein Eng. 8:425-435, 1995.
5. 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.
6. Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72, 1994.
7. Reczko, M., Bohr, H. The DEF data base of sequence based protein fold class predictions. Nucleic Acids Res. 22:3616-3619, 1994.
8. 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.
9. Nishikawa, K., Kubota, Y., Ooi, T. Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution. J. Biochem. 94:981-995, 1983.
10. 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.
11. 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.
12. Chou, P.Y. Prediction of protein structural classes from amino acid composition. In: 'Prediction of Protein Structure and Principles of Protein Conformation.' Fasman, G.D. (ed.). New York: Plenum Press, 1989:549-586.
13. Eisenhaber, F., Frommel, C., Argos, P. Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class. Proteins 25:169-179, 1996.
14. Berry, M.W., Dumais, S.T., O'Brien, G.W. Using linear algebra for intelligent information retrieval. SIAM Rev. 37:573-595, 1995.
15. Harary, F. 'Graph Theory.' Reading MA: Addison-Wesley, 1971.
16. Jernigan, R.L. Generating general shapes and conformations with regular lattices, for compact proteins. In: Structure & Function' R.H.Sarma, Sarma, M.H. (ed.). Adenine Press, Schenectady, NY, Vol. 2 1992:169-182.
17. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S. Principles of protein folding. A perspective from simple exact models. Protein Sci. 4:561-602, 1995.
18. Li, H., Helling, R., Tang, C., Wingreen, N. Emergence of preferred structures in a simple model of protein folding. Science 273:666-669, 1996.
19. Bernstein, F., Koetzle, T., Williams, G., Meyer, E., Brice, M., Rodgers, J., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Databank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
20. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. 'Protein Data Bank, Crystallography Databases-Information Content Software Systems, Scientific Applications' Allen, F.H., Bergerhoff, G., Sievers, R. (eds.). Bonn, Cambridge, and Chester: Data Commission of the International Union of Crystallography, 1987:107.
21. Chou, K., Zhang, C. Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 30:275-439, 1995.
22. Jernigan, R.L., Bahar, I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6:195-209, 1996.
23. Bahar, I., Jernigan, R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214, 1997.
24. Bahar, I., Jernigan, R.L. Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. Biophys. J. 66:467-477, 1994.
25. Schuler, K.E. (ed.) Stochastic processes in chemical physics. 'Advances in Chemical Physics.' Prigogine, I., Rice, S. (series eds.). Vol. 15. New York: Interscience, 1969.
26. Miyazawa, S., Jernigan, R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:623-644, 1996.
27. Garnier, J., Robson, B. The GOR method for predicting secondary structures in proteins. In: 'Prediction of Protein Structure and Principles of Protein Conformation.' Fasman, G.D. (ed.). New York: Plenum Press, 1989:417-465.
28. Deléage, G., Roux, B. Use of class prediction to improve protein secondary structure prediction. In: 'Prediction of Protein Structure and Principles of Protein Conformation.' Fasman, G.D. (ed.). New York: Plenum Press, 1989:587-597.
29. Eisenhaber, F., Imperiale, F., Argos, P., Frommel, C. Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods. Proteins 25:157-168, 1996.
30. Naor, D., Fischer, D., Jernigan, R.L., Wolfson, H.J., Nussinov, R. Amino acid pair interchanges at spatially conserved locations. J. Mol. Biol. 256:924-938, 1996.
31. Chandonia, J.-M., Karplus, M. Neural networks for secondary structure and structural class predictions. Protein Sci. 4:275-285, 1995.
32. Rahman, R.S., Rackovsky, S. Protein sequence randomness and sequence/structure correlations. Biophys. J. 68:1531-1539, 1995.
33. Pillai, K.C.S. Mahalanobis, Prasanta Chandra. In: Encyclopedia of Statistical Sciences.' Kotz, S., Johnson, N.L. (ed.). New York: John Wiley & Sons, 1985:176-181.