Biopolym. Cell. 1992; 8(5):21-31.
Структура та функції біополімерів
Передбачення вторинної структури білків
1Мальченко С. З., 1Чащин М. О.
  1. Інститут молекулярної біології і генетики НАН України
    Вул. Академіка Заболотного, 150, Київ, Україна, 03680

Abstract

Проаналізовано ряд методів, що належать до різних класів (статистичні методи, методи подібності послідовностей, фізико-хімічні методи та комбіновані методи), визначено переваги й обмеження існуючих підходів до передбачення вторинної структури білків. Запропоновано гіпотезу про можливий напрямок прогресу у цій галузі, яка полягає у виявленні та аналізі інформаційних сайтів білків, розробці логічних методів аналізу вторинної структури білків.

References

[1] Solov'yev VV, Salamov AA, Salikhanova AK. Computer system for the study of the structural organization of globular proteins. Computer analysis of the structure, function and evolution of the genet. macromolecules probl. intellectualization. Novosibirsk, 1989; 111-54.
[2] Shestopalov BV. Algorithm protein secondary structure prediction by doublet code method. III Proc. All-Unian. "Theor. research and data basees on mol biol and Genet ": Proc. of reports. Novosibirsk, 1988: 57-60.
[3] Biou V, Gibrat JF, Levin JM, Robson B, Garnier J. Secondary structure prediction: combination of three different methods. Protein Eng. 1988;2(3):185-91.
[4] Bohr H, Bohr J, Brunak S, Cotterill RM, Fredholm H, Lautrup B, Petersen SB. A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Lett. 1990;261(1):43-6.
[5] Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry. 1974;13(2):222-45.
[6] Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45-148.
[7] Computational molecular biology: Sources and methods for sequence analysis. Ed. Ar. M. Lesk. Oxford : Univ. press, 1988. 537 p.
[8] Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978;120(1):97-120.
[9] Garnier J, Robson B. The GOR method for predicting secondary structures in proteins. Prediction of protein structure and the principles of protein conformation. Ed. G. D. Fasman. New York: Plenum publ. press corporation, 1989: 417-65.
[10] Garnier J. Protein structure prediction. Biochimie. 1990;72(8):513-24. Review.
[11] Garnier J, Levin JM, Gibrat JF, Biou V. Secondary structure prediction and protein design. Biochem Soc Symp. 1990;57:11-24.
[12] Garnier J, Levin JM. The protein structure code: what is its present status? Comput Appl Biosci. 1991;7(2):133-42.
[13] Gibrat JF, Garnier J, Robson B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J Mol Biol. 1987;198(3):425-43.
[14] Holley LH, Karplus M. Protein secondary structure prediction with a neural network. Proc Natl Acad Sci U S A. 1989;86(1):152-6.
[15] Hopfield JJ. Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci U S A. 1982;79(8):2554-8.
[16] Hopfield JJ. Neurons with graded response have collective computational properties like those of two-state neurons. Proc Natl Acad Sci U S A. 1984;81(10):3088-92.
[17] Hopfield JJ, Tank DW. Computing with neural circuits: a model. Science. 1986;233(4764):625-33.
[18] Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A. 1984;81(4):1075-8.
[19] Levin JM, Garnier J. 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. 1988;955(3):283-95.
[20] Lim VI. Algorithms for prediction of α-helical and β-structural regions in globular proteins. J Mol Biol. 1974;88(4):873–94.
[21] Nagano K. Triplet information in helix prediction applied to the analysis of super-secondary structures. J Mol Biol. 1977;109(2):251-74.
[22] Nishikawa K, Ooi T. Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods. Biochim Biophys Acta. 1986;871(1):45-54.
[23] Nishikawa K, Noguchi T, Kotiishi Y. Highly reliable secondary structure prediction of proteins by a new joint method. Prot Engng, 1990. 3(4):283-4.
[24] Ptitsyn OB, Finkelstein AV. Theory of protein secondary structure and algorithm of its prediction. Biopolymers. 1983;22(1):15-25.
[25] Ptitsyn OB, Finkelstein AV. Prediction of protein secondary structure based on physical theory. Histones. Protein Eng. 1989;2(6):443-7.
[26] Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol. 1988;202(4):865-84.
[27] Schiffer M, Edmundson AB. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J. 1967;7(2):121-35.
[28] Sternberg MJ, Islam SA. Local protein sequence similarity does not imply a structural relationship. Protein Eng. 1990;4(2):125-31.
[29] Sweet RM. Evolutionary similarity among peptide segments is a basis for prediction of protein folding. Biopolymers. 1986;25(8):1565-77.