Correlations in protein sequences and property codes

Journal of Theoretical Biology

Volumn 190, Issue 4, 1998, Pages 341-353

  Weiss, Olaf ^a   Herzel, Hanspeter ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; CLUSTER ANALYSIS; CORRELATION FUNCTION; HYDROPHOBICITY; OSCILLATION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SIMULATION; SYSTEM ANALYSIS;

EID: 0032554318     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1997.0560     Document Type: Article

References (36)

1. BERMAN, A., KOLKER, E. & TRIFONOV, E. N. (1994). Underlying order in protein sequence organization. Proc. Natl. Acad. Sci. U.S.A. 91, 4044-4047.
2. CASARI, G. & SIPPL, M. J. (1991). Structure-derived hydrophobic potential. J. Mol. Biol. 224, 725-732.
3. COHEN, C. & PARRY, D. A. D. (1994). α-Helical coiled coils: more facts and better predictions. Science 263, 488-489.
4. DILL, K, A., BROMBERG, S., YUE, K., FIEBIG, K. M., YEE, D. P., THOMAS, P, D. & CHAN, H. S. (1995). Principles of protein folding - a perspective from simple exact models. Protein Science 4, 561-602.
5. EBELING, W., FEISTEL, R. & HERZEL, H. (1987). Dynamics and complexity of biomolecules. Physica Scripta 35, 761-768.
6. EISENHABER, F., PERSSON, B. & ARGOS, P. (1995). Protein structure prediction: recognition of primary, secondary and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Bio. 30, 1-94.
7. EISENHABER, F., IMPERALE, F., ARGOS, P. & FRÖMMEL (1996). Prediction of secondary structural content of proteins form their amino acid composition alone. I. New analytic vector decomposition methods. Proteins 25, 157-168.
8. FISHER, R. A. (1915). Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population. Biometrica 10, 507-521.
9. FRISHMAN, D. & ARGOS, P. (1997). Seventy-five percent accuracy in protein secondary structure prediction. Proteins 27, 329-335.
10. GARNIER, J., OSGUTHORPE, D. J. & 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.
11. GROSSE, I. (1995). Statistical Analysis of Biosequences. Berlin: Diplomthesis Humboldt University.
12. HERZEL, H. & GROSSE, I. (1995). Measuring correlations in symbol sequences. Physica A 216, 518-542.
13. HERZEL, H., SCHMITT, A. O. & EBELING, W. (1994). Finite sample effects in sequence analysis. Chaos, Solit. & Fractals 4, 97-113.
14. HERZEL, H. & GROSSE, I. (1997). Correlations in DNA sequences -the role of protein coding segments. Phys. Rev. E 55, 800-810.
15. HOBOHM, U. & SANDER, C. (1995). A sequence property approach to searching protein databases. J. Mol. Biol. 251, 390-399.
16. JOHNSON, M. S. & OVERINGTON, J. P. (1993). A structural basis for sequence comparisons. J. Mol. Biol. 233, 716-738.
17. KAMTEKAR, S., SCHIFFER, J. M., XIONG, H., BABIK, J. M. & HECHT, M. H. (1993). Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680-1685.
18. KANEHISA, M. I. & TSONG, T. Y. (1980). Hydrophobicity and protein structure. Biopolymers 19, 1617-1628.
19. KOLKER, E. & TRIFONOV, E. N. (1995). Periodic recurrence of methionines - fossil of gene fusion. Proc. Natl. Acad. Sci. U.S.A. 92, 557-560.
20. KYTE, J. & DOOLITTLE, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
21. KULLBACK, S. (1959). Information Theory and Statistics. New York: Wiley.
22. LANDSCHULZ, W. H., JOHNSON, P. F. & MCNIGHT, S. L. (1988). The Leucine Zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 1759-1764.
23. LEWIN, B. (1994). Genes V. Oxford: Oxford University Press.
24. LI, W. & KANEKO, K. (1992). Long-range correlation and partial 1/fα spectrum in a noncoding DNA sequence. Europhys. Lett. 17, 655-660.
25. LI, H., TANG, C. & WINGREEN, N. (1995). Dominant Driving Force for Protein Folding - A Result form Analyzing the Statistical Potential. Phys. Rev. Lett. 79, 765-768.
26. MACCHIATO, M. F., CUOMO, V. & TRAMONTANO, A. (1985). Determination of the autocorrelation orders of proteins. Eur. J. Biochem. 149, 375-379.
27. MURZIN A. G., BRENNER S. E., HUBBARC T. & CHOTHIA C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
28. NAOR, D., FISCHER, D., JERNIGAN, R. L., WOLFSON, H. J. & NUSSINOV, R. (1996). Amino acid pair interchanges at spatially conserved locations. J. Mol. Biol. 256, 924-938.
29. PANDE, S. V., GROSBERG, A. Y. & TANAKA, T. (1994). Nonrandomness in protein sequences: evidence for a physically driven stage of evolution? Proc. Natl. Acad. Sci. U.S.A. 91, 12972-12975.
30. RANI, M. & MITRA, C. K. (1996). Pair preferences: a quantitative measure of regularities in protein sequences. J. Biomol. Struct. Dynamics 13, 935-944.
31. SCHMITT, A. O., KOLKER, E. & TRIFONOV, E. N. (1997). Hidden infrastructure of protein sequences. In: Mathematical Modeling and Scientific Computing. St Louis, MI: Principia Scientia.
32. SCHNEIDER, G., SCHUCHHARDT, J. & WREDE, P. (1995). Development of simple fitness landscapes for peptides by artificial neural filter systems. Biol. Cybern. 73, 245-254.
33. WEISS, O. & HERZEL, H. (1998). Measuring correlations in protein sequences. Zeitschr. Phys. Chem. 204, 183-197.
34. WHITE, S. H. & JACOBS, R. E. (1993). The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern proteins. J. Mol. Evol. 36, 79-95.
35. WHITE, S. H. (1994). Global statistics of protein sequences: implications for the origin, evolution, and prediction of structure. Annu. Rev. Biophys. Biomolec. Struc. 23, 407-439.
36. WOESE, C. R., DUGRE, D. H., SAINGER, W. C. & DUGRE, S. A. (1966). The molecular basis of the genetic code. Proc. Natl. Acad. Sci. U.S.A. 55, 966-974.