Protein contact map prediction based on an ensemble learning method

Proceedings - 2009 International Conference on Computer Engineering and Technology, ICCET 2009

Volumn 2, Issue , 2009, Pages 205-209

  Habibi, Narjes Khatoon ^a   Saraee, Mohammad Hossein ^a  

^a ISFAHAN UNIVERSITY OF TECHNOLOGY   (Iran)

Author keywords

Bioinformatic; Contact map prediction; Ensemble learning; Neural network; Protein tructure prediction

Indexed keywords

CONTACT MAP PREDICTION; CONTACT MAPS; ENSEMBLE LEARNING; PERFORMANCE IMPROVEMENTS; PROTEIN 3-D STRUCTURE; SPATIAL STRUCTURE;

BIOINFORMATICS; NEURAL NETWORKS; THREE DIMENSIONAL;

EDUCATION;

EID: 65949094811     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICCET.2009.58     Document Type: Conference Paper

References (25)

1. N. Gupta, N. Mangal and S. Biswas, "Evolution and similarity evaluation of protein structures in contact map space", Proteins, vol 59(2), pp. 196-204, 2005.
2. U. Gobel, C. Sander, R. Schneider, A. Valencia, "Correlated mutations and residue contacts in proteins", Proteins, vol.18(4). pp. 309-317, 1994.
3. O. Olmea and A. Valencia, "Improving contact predictions by the combination of correlated mutations and other sources of sequence information", Folding and Design, vol.2(3), pp. 25-32, 1997.
4. G. Z. Zhang and K. Han, "Hepatitis C virus contact map prediction based on binary encoding strategy", Computational Biology and Chemistry, vl. 31,pp. 233-238, 2007.
5. G. Shackelford and K. Karplus, "Contact prediction using mutual information and neural nets", Proteins, vol 69 suppl 8, pp. 159-164, 2007.
6. Y. Zhao and G. Karypis, "Prediction of Contact Maps Using Support Vector Machines", in proc of third IEEE Symposium on Bioinformatics and Bioengineering, pp. 22-23, 2003.
7. A. Vullo, I. Walsh and G. Pollastri, "A two-stage approach for improved prediction of residue contact maps", BMC Bioinformatics, vol.7:180, 2006.
8. P. Fariselli, O. Olmea, A. Valencia and R. Casadio, "Prediction of contact maps with neural networks and correlated mutations", Protein Engineering, vol 14(11), pp. 835-843, 2001.
9. M. Zaki, S. Jin, and C. Bystroff, "Mining residue contacts in proteins using local structure predictions", in proc. of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering (BIBE 2000), Washington, D. C., pp. 168-175, 2000.
10. S. Wu and Y. Zhang, "A comprehensive assessment of sequence-based and template-based methods for protein contact prediction", Bioinformatics, vol.24, 924-931, 2008.
11. P. Fariselli and R. Casadio, "A neural network based predictor of residue contacts in proteins", Protein Engineering, vol.12(1), pp. 15-21, 1999.
12. A. Robins, "Sequential learning in neural networks: A review and discussion of psedorehearsal based methods", Intellignet Data Analysis, vol.8(3), pp. 301-322, 2004.
13. C. Ji and D. Psaltis, "Capacity of Two-Layer Feedforward Neural Networks with Binary Weights", IEEE TRANSACTIONS ON INFORMATION THEORY, vol.44, 1998.
14. K. Mahdaviani, H. Mazyar, S. Majidi and M. H.Saraee, "A Method to Resolve the Overfitting Problem in Recurrent Neural Networks for Prediction of Complex Systems' Behavior", in the proc. of IEEE international joint conf. on neural networks (IJCNN 2008),Hong Kong, 2008.
15. V. Tresp, "Committee machines", Handbook for Neural Network Signal Processing, CRC Press, 2001.
16. K. Nakai, A. Kidera and M. Kanehisa, "Cluster analysis of amino acid indices for prediction of protein structure and function", Protein Engineering, vol.2, pp. 93-100, 1988.
17. K. Tomii and M. Kanehisa, "Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins", Protein Engineering, vol.9, pp. 27-36, 1996.
18. S. Kawashima, H. Ogata and M. Kanehisa, "AAindex: amino acid index database", Nucleic Acids Research, vol.27, pp. 368-369, 1999.
19. S. Kawashima and M. Kanehisa, "AAindex: amino acid index database", Nucleic Acids Research, vol.28, pp. 374, 2000.
20. S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama and M. Kanehisa, "AAindex: amino acid index database, progress report 2008", Nucleic Acids Research, vol.36, pp. 202-205, 2008.
21. K. Bryson, L. J. McGuffin, R. L. Marsden, J. J. Ward, J. S. Sodhi and D. T. Jones, "Protein structure prediction servers at University College London", Nucleic Acids Research, vol.33(Web Server issue), pp. 36-38, 2005.
22. D. T. Jones, "Protein secondary structure prediction based on position-specific scoring matrices", Molecular Biology, vol.292, pp. 195-202, 1999.
23. C. Sander and R. Schneider, "Database of homology-derived protein structures", Proteins, Structure, Function and Genetics", vol. 9, pp. 56-68, 1991.
24. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I.N. Shindyalov and P.E. Bourne, "The Protein Data Bank", Nucleic Acids Research, vol.28, pp. 235-242, 2000.
25. U.Hobohm, M.Scharf, R.Schneider and C.Sander, "Selection of a representative set of structures from the Brookhaven Protein Data Bank", Protein Science, vol.1, pp. 409-417, 1992.