Predicting secondary structures of proteins

IEEE Engineering in Medicine and Biology Magazine

Volumn 24, Issue 3, 2005, Pages 88-94

  Błazewicz, Jacek ^a,b   Hammer, Peter L ^c   Łukasiak, Piotr ^a  

^a POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b Institute of Computing Science   (Poland)

^c the State University of New Jersey   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; PROTEIN;

ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; PROTEIN ANALYSIS; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 20644432217     PISSN: 07395175     EISSN: None     Source Type: Journal    
DOI: 10.1109/MEMB.2005.1436465     Document Type: Review

References (33)

1. B. Rost, C. Sander, "Prediction of protein secondary structure at better than 70% accuracy," J. Mol. Biol., vol. 232, pp. 584-599, 1993.
2. C.B. Anfinsen, "Principles that govern the folding of protein chains," Science, vol. 181, pp. 223-230, 1973.
3. J. Garnier, D. Osguthorpe, and B. Robson, "Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins," J. Mol. Biol., vol. 120, pp. 97-120, 1978.
4. V. Lim, "Algorithms for prediction of α-helical and β-structural regions in globular proteins," J. Mol. Biol., vol. 88, pp. 873-894, 1974.
5. B. Rost, "PHD: Predicting one-dimensional protein structure by profile based neural networks," Meth. Enzymol., vol. 266, pp. 525-539, 1996.
6. X. Zhang, J.P. Mesirov, and D.L. Waltz, "Hybrid system for protein secondary structure prediction," J. Mol. Biol., vol. 225, pp. 1049-1063, 1992.
7. J.A. Cuff and G.J. Barton, "Evaluation and improvement of multiple sequence methods for protein secondary structure prediction," Proteins: Struct. Funct. Genet., vol. 34, pp. 508-519, 1999.
8. D. Jones, "Protein secondary structure prediction based on position-specific scoring matrices," J. Mol. Biol., vol. 292, pp. 195-202, 1999.
9. J.A. Cuff and G.J. Barton, "Application of multiple sequence alignment profiles to improve protein secondary structure prediction," Proteins, vol. 40, pp. 502-511, 2000.
10. P. Baldi, S. Brunak, P. Frasconi, G. Soda, and G. Pollastri, "Exploiting the past and the future in protein secondary structure prediction," Bioinformatics, vol. 15, pp. 937-946, 1999.
11. A. Salamov and V. Solovyev, "Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignment," J. Mol. Biol., vol. 247, pp. 11-15, 1995.
12. J.A. Cuff, M.E. Clamp, A.S. Siddiqui, M. Finlay, and G.J. Barton, "Jpred: A consensus secondary structure prediction server," Bioinformatics, vol. 14, pp. 892-893, 1998.
13. R. King and M. Sternberg, "Identification and application of the concepts important for accurate and reliable protein secondary structure prediction," Prot. Sci., vol. 5, pp. 2298-2310, 1996.
14. D. Frishman and P. Argos, "Seventy-five percent accuracy in protein secondary structure prediction" Proteins, vol. 27, pp. 329-335, 1997.
15. B. Rost, C. Sander, and R. Schneider, "Redefining the goals of protein secondary structure prediction," J. Mol. Biol., vol. 235, pp. 13-26, 1994.
16. A. Zemla, C. Venclovas, K. Fidelis, and B. Rost, "A modified definition of SOV, a segment based measure for protein secondary structure prediction assessment," Proteins: Struct. Funct. Genet., vol. 34. pp. 220-223, 1999.
17. P.L. Hammer, "Partially defined boolean functions and cause-effect relationships," presented at the International Conference on Multi-Attribute Decision Making Via OR-Based Expert Systems, Passau, Germany, 1986.
18. E. Boros, P.L. Hammer, T. Ibaraki, A. Kogan, E. Mayoraz, and I. Muchnik, "An implementation of logical analysis of data," Rutcor Res. Rep., Rep. 22-96, 1996.
19. E. Boros, P.L. Hammer, A. Kogan, E. Mayoraz, and I. Muchnik, "Logical analysis of data - overview," Rutcor Res. Rep., Rep. 1-94, 1994.
20. Y. Crama, P.L. Hammer, and T. Ibaraki, "Cause-effect relationships and partally defined Boolean functions," Ann. Oper. Res., vol. 16, pp. 299-326, 1998.
21. E, Mayoraz, "C++ tools for logical analysis of data," Rutcor Research Report, Rep. 1-95, 1995.
22. J. Blazewicz, P.L. Hammer, and P. Lukastak, "Logical Analysis of Data as a predictor of protein secondary structures," in Bioinformatics of Genome Regulations and Structure, N. Kolchanov and R. Hofestaedt, Eds. Norwell, MA: Kluwer, 2004, pp. 145-154.
23. O. Ekin, P.L. Hammer, and A. Kogan, "Convexity and logical analysis of data," Rutcor Research Report, Rep. 5-98, 1998.
24. E. Boros, P.L. Hammer, T. Ibaraki, and A. Kogan, "Logical analysis of numerical data," Rutcor Research Report, Rep. 4-97, 1997.
25. J. Blazewicz, P.L. Hammer, and P. Lukasiak, "Prediction of protein secondary structure using Logical Analysis of Data algorithm," Comput. Methods Sci. Technol., vol. 7, no. 1, pp. 7-25, 2001.
26. C.W. Hsu and C.J. Lin, "A comparison of methods for multi-class support vector machines," IEEE Trans. Neural Networks, vol. 13, pp. 415-425, 2002.
27. S.J. Hua and Z.R. Sun, "A novel method of protein secondary structure prediction with high overlap measure: Support vector machine approach," J. Mol. Biol., vol. 308, pp. 397-407, 2001.
28. W. Kabsch and C. Sander, "Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features," Biopolymers, vol. 22, pp. 2577-2637, 1983.
29. D. Frishman and P. Argos, "Knowledge based secondary structure assignment," Proteins: Struct. Funct. Genet., vol. 23, pp. 566-579, 1995.
30. F.M. Richards and C.E. Kundrot, "Identification of structural motifs from protein coordinate data: Secondary structure and first level supersecondary structure" Proteins: Struct. Funct. Genet., vol. 3, pp. 71-84, 1988.
31. R.D. King and M.J.E. Sternberg, "Machine learning approach for the prediction of protein secondary structure," J. Mol. Biol., vol. 216, pp. 441-457, 1990.
32. J.W. Grzymala-Busse, "LERS - A system for learning from examples based on rough sets," in Intelligent Decision Support - Handbook of Applications and Advances of the Rough Set Theory, R. Slowinski, Ed. Norwell, MA: Kluwer, 1992, pp. 3-18.
33. J.W. Grzymala-Busse and J. Stefanowski, "Three approaches to numerical attribute discretization for rule induction," Int. J. Intell. Syst., vol. 16, pp. 29-38, 2001.