How good is prediction of protein structural class by the component- coupled method?

Proteins: Structure, Function and Genetics

Volumn 38, Issue 2, 2000, Pages 165-175

  Wang, Zhi Xin ^a   Yuan, Zheng ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

Author keywords

+ domains; domains; domains; domains; Amino acid composition; Bayes decision rule; Jack knife analysis; SCOP database

Indexed keywords

AMINO ACID COMPOSITION; ANALYTIC METHOD; ARTICLE; BAYES THEOREM; DATA BASE; DISCRIMINANT ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; DATABASES, FACTUAL; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0034141493     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000201)38:2<165::AID-PROT5>3.0.CO;2-V     Document Type: Article

References (37)

1. Levitt M, Chothia C. Structural patterns in globular proteins. Nature 1976;261:552-558.
2. Richardson JS, Richardson DC. Principles and patterns of protein conformation. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York:Plenum Press; 1989. p 1-98.
3. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: A structural classification of protein database for the investigation of sequence and structures. J Mol Biol 1995;247:536-540.
4. Michie AD, Orengo CA, Thornton JJ. Analysis of domain structural class using an automated class assignment protocol. J Mol Biol 1996;262:168-185.
5. Deleage G, Roux B. Use of class prediction to improve protein secondary structure prediction. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press; 1989. p 417-465.
6. Kneller DG, Cohen FE, Langridge R. Improvements in protein secondary-structure prediction by enhanced neural networks. J Mol Biol 1990;214:171-182.
7. Klein P, Delisi C. Prediction of protein structural class from amino acid sequence. Biopolymers 1986;25:1659-1672.
8. Klein P. Prediction of protein structural class by discriminant analysis. Biochim Biophys Acta 1986;874:205-215.
9. Chou PY. Amino acid composition of four classes of proteins. In: Abstracts of papers, Part I, Second Chemical Congress of the North American Continent. Las Vegas, 1980.
10. Chou PY. Prediction of protein structural classes from amino acid composition. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press; 1989. p 549-586.
11. Nakashima H, Nishikawa K, Ooi T. The folding type of a protein is relevant to the amino acid composition. J Biochem 1986;99:153-162.
12. Zhang CT, Chou KC. An optimization approach to predicting protein structural class from amino acid composition. Protein Sci 1992;1:401-408.
13. Chou KC, Zhang CT. A new approach to predicting protein folding types. J Protein Chem 1993;12:169-178.
14. Chou KC, Zhang CT. Predicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem 1994;269:22014-22020.
15. Chou KC. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 1995;21:319-344.
16. Chou KC, Zhang CT. Prediction of protein structural classes. Crit Rev Biochem Mol Biol 1995;30:275-349.
17. Eisenhaber F, Frömmel C, Argos P. Prediction of secondary structural content of proteins from their amino acid composition along. II. The paradox with secondary structural class. Proteins 1996;25:169-179.
18. Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997;29:172-185.
19. Chou KC, Liu WM, Maggiora GM, Zhang CT. Prediction and classification of domain structural classes. Proteins 1998;31:97-103.
20. Chou KC, Maggiora GM. Doman structural class prediction. Protein Eng 1998;11:523-538.
21. Tou JT, Gonzalez RC. Pattern recognition principles. London: Addison-Wesley Publishing Company; 1974.
22. Duda RO, Hart PE. Pattern classification and scene analysis. New York: John Wiley & Sons; 1973.
23. Andrew HC. Introduction to mathematical techniques in pattern recognition. New York: John Wiley & Sons; 1972.
24. DeGroot MH. Probability and statistics. 2nd ed. Reading, MA: Addision-Wesley Publishing Co.; 1986. p 267-278.
25. Zhang CT, Chou KC. Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. Biophys J 1992;63:1523-1529.
26. Anderson TW. Introduction to multivariate statistics. New York: John Wiley & Sons; 1958.
27. Sander C, Schneider R. Database of homology-derived protein structures and structural meaning of sequence alignment. Proteins 1991;9:56-58.
28. Blundell TL, Johnson MS. Catching a common fold. Protein Sci 1993;2:877-883.
29. Flores TP, Orengo CA, Moss D, Thornton JM. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993;2:1811-1826.
30. Hilbert M, Bohm G, Jaenicke R. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 1993;17:138-151.
31. Brenner SE, Chhothia C, Hubbard TJP. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998;95: 6073-6078.
32. Kabsch W, Sander C. Dictionary of protein secondary structures: pattern recognitioin of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
33. Metfessel BA, Saurugger PN, Connelly DP, Rich SS. Cross-validation of protein structural class prediction using statistical clustering and neural networks. Protein Sci 1993;2:1171-1182.
34. Chandonia JM, Karplus M. Neural networks for secondary structure and structural class predictions. Protein Sci 1995;4:275-285.
35. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
36. Levin JM, Pascarella S, Argos P. Garnier J. Quantification of secondary structure prediction improvement using multiple alignments. Protein Eng 1993;6:849-854.
37. Boberg J, Salakoski T, Vihinen M. Accurate prediction of protein secondary structural class with fuzzy structural vectors. Protein Eng 1995;8:505-512.