Predicting protein secondary structure with probabilistic schemata of evolutionarily derived information

Protein Science

Volumn 6, Issue 9, 1997, Pages 1963-1975

  Thompson, Michael J ^a   Goldstein, Richard A ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Bayesian statistics; Evolutionary information; Mutual information; Probabilistic schemata; Secondary structure prediction

Indexed keywords

ACCURACY; AMINO ACID SUBSTITUTION; ARTICLE; DATA BASE; EVOLUTION; NERVE CELL NETWORK; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROBABILITY; PROTEIN SECONDARY STRUCTURE; STATISTICAL ANALYSIS; STRUCTURE ACTIVITY RELATION;

EID: 0030874702     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060917     Document Type: Article

References (44)

1. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. 1987. Protein data bank. In: Allen FH, Bergerhoff G, Sievers R, eds. Crystallographic databases -Information content, software systems, scientific applications. Bonn: Data Commission of the International Union of Crystallography. pp 107-132.
2. Aronson HEG, Royer WE, Hendrickson WA. 1994. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Protein Sci 3:1706-1711.
3. Asai K, Haymizu S, Handa K. 1993. Prediction of protein secondary structure by the hidden Markov model. CABIOS 2:141-146.
4. Benner SA. 1989. Patterns of divergence in homologous proteins as indicators of tertiary and quaternary structure. Adv Enz Regul 28:219-236.
5. Benner SA. 1992. Predicting de novo the folded structure of proteins. Curr Opin Struc Biol 2:402-412.
6. Benner SA, Chelvanayagam G, Turcotte M. 1997. Bona fide predictions of protein secondary structure using transparent analyses of multiple-sequence alignments. Chem Rev. Forthcoming.
7. Benner SA, Gerloff DL. 1993. Predicting the conformation of proteins: Man versus machine. FEBS Lett 325:29-33.
8. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
9. Cover TM, Thomas JA. 1991. Elements of information theory. New York: John Wiley & Sons, Inc.
10. Gibrat JF, Garnier J, Robson B. 1987. Further developments of protein secondary structure prediction using information theory. J Mol Biol 198:425-443.
11. Goldman N, Thorne JL, Jones DT. 1996. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol 263:196-208.
12. Goldstein RA, Luthey-Schulten ZA, Wolynes PG. 1992. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc Natl Acad Sci USA 89:9029-9033.
13. Goldstein RA, Lulhey-Schulten ZA, Wolynes PG. 1994. A Bayesian approach to sequence alignment algorithms for protein structure recognition. In: Proc. 27th Annual Hawaii International Conference on System Sciences. Los Alamitos: IEEE Computer Society Press. pp 306-315.
14. Govindarajan S, Goldstein RA. 1996. Why are some protein structures so common? Proc Natl Acad Sci. USA 93:3341-3345.
15. Govindarajan S, Goldslein RA. 1997. Evolution of model proteins. Proteins. Forthcoming.
16. Harvey PH, Pagel MD. 1991. Comparative methods for explaining adaptation. Nature (London) 351:619-624.
17. Hobohm U, Sander C. 1994. Enlarged representative set of protein structures. Protein Sci 3:522-524.
18. Holland J. 1992. Adaptation in natural and artificial systems. Cambridge, Massachusetts: Massachusetts Institute of Technology Press.
19. Kabsch W, Sander C. 1983. Dictionary of protein secondary structures: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
20. King RD, Sternberg MJE. 1996. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci 5:2298-2310.
21. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology. J Mol Biol 235:1501-1531.
22. Lim V. 1974. Algorithms for prediction of α-helical and β-structural regions in globular proteins. J Mol Biol 88:873-894.
23. Mamitsuka H. 1995. Representing inter-residue dependencies in protein sequences with probabilistic networks. CABIOS 11:413-422.
24. Matthews BW. 1975. Comparison of predicted and observed secondary structure of T4 phage lysozyme. Biocim Biophys Acta 405:402-451.
25. Maxfield FR, Scheraga HA. 1979. Improvements in the prediction of protein backbone topography by reduction of statistical errors. Biochem 18:697-704.
26. Mehta PK, Heringa J, Argos P. 1995. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Sci 4:2517-2525.
27. Richardson JS, Richardson DC. 1988. Amino acid preferences for specific locations at the ends of α-helices. Science 240:1648-1652.
28. Riis SK, Krogh A. 1996. Improving prediction of protein secondary structure using structured neural networks and multiple-sequence alignments. J Comput Biol 3:163-183.
29. Robson B. 1974. Analysis of the code relating sequences to conformation in globular proteins. Theory and application of expected information. Biochem J 141:853-867.
30. Rost B, Sander C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232:584-599.
31. Rost B, Sander C. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72.
32. Salamov A, Solovyev V. 1995. Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple-sequence alignments. J Mol Biol 247:11-15.
33. Sander C, Schneider R. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
34. Shannon CE, Weaver W. 1949. The mathematical theory of communication. Urbana, Illinois: University of Illinois Press.
35. Shrake A, Rupley JA. 1973. Environment and exposure to solvents of protein atoms: Lysozyme and insulin. J Mol Biol 79:351-371.
36. Sjolander K, Karplus K, Brown M, Hughey R, Krogh A, Mian I, Haussler D. 1996. Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. CABIOS 72:327-345.
37. Stolorz P, Lapedes A, Xia Y. 1992. Predicting protein secondary structure using neural nets and statistical methods. J Mol Biol 225:363-377.
38. Stultz CM, White JV, Smith TF. 1993. Structural analysis based on state-space modeling. Protein Sci 2:305-314.
39. Thompson MJ, Goldstein RA. 1996a. Constructing amino acid residue substitution classes maximally indicative of local protein structure. Proteins 25:28-37.
40. Thompson MJ, Goldstein RA. 1996b. Predicting solvent accessibility: Higher accuracy using Bayesian statistics and optimized residue substitution classes. Proteins 25:38-47.
41. Wako H, Blundell T. 1994a. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes. J Mol Biol 238:682-692.
42. Wako H, Blundell T. 1994b. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures. J Mol Biol 238:693-708.
43. Yi TM, Lander ES. 1993. Protein secondary structure prediction using nearest-neighbor methods. J Mol Biol 232:1117-1129.
44. Zhang X, Mesirov JP, Waltz DL. 1992. Hybrid system for protein secondary structure prediction. J Mol Biol 225:1049-1063.