Prediction of protein secondary structures with a novel kernel density estimation based classifier

BMC Research Notes

Volumn 1, Issue , 2008, Pages

  Chang, Darby Tien Hao ^a   Ou, Yu Yen ^b   Hung, Hao Geng ^c   Yang, Meng Han ^c   Chen, Chien Yu ^c   Oyang, Yen Jen ^c  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b YUAN ZE UNIVERSITY   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77952008492     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-1-51     Document Type: Article

References (20)

1. Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis. I Eidhammer I Jonassen WR Taylor, Chichester: John Wiley & Sons Ltd 2004
2. Introduction to Bioinformatics. A Lesk, Oxford: Oxford University Press 2005
3. Bioinformatics: the Machine Learning Approach. P Baldi S Brunak, Cambridge: MIT Press 2001
4. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. JA Cuff GJ Barton, Proteins-Structure Function and Genetics 2000 40 3 502 511 10.1002/1097-0134(20000815)40:3<502::AID- PROT170>3.0.CO;2-Q
5. The PSIPRED protein structure prediction server. LJ McGuffin K Bryson DT Jones, Bioinformatics 2000 16 4 404 405 10.1093/bioinformatics/16.4.404 10869041
6. Secondary structure prediction with support vector machines. JJ Ward LJ McGuffin BF Buxton DT Jones, Bioinformatics 2003 19 13 1650 1655 10.1093/bioinformatics/btg223 12967961
7. HYPROSP: a hybrid protein secondary structure prediction algorithm - a knowledge-based approach. KP Wu HN Lin JM Chang TY Sung WL Hsu, Nucleic Acids Research 2004 32 17 5059 5065 15448186 10.1093/nar/gkh836 (Pubitemid 39445492)
8. HYPROSP II - A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. HN Lin JM Chang KP Wu TY Sung WL Hsu, Bioinformatics 2005 21 15 3227 3233 10.1093/bioinformatics/ bti524 15932901
9. Improving the accuracy of protein secondary structure prediction using structural alignment. S Montgomerie S Sundararaj WJ Gallin DS Wishart, BMC Bioinformatics 2006 7 301 16774686 10.1186/1471-2105-7-301 (Pubitemid 44262650)
10. Achieving 80% Ten-fold Cross-validated Accuracy for Secondary Structure Prediction by Large-scale Training. O Dor Y Zhou, Proteins: Structure, Function, and Bioinformatics 2007 66
11. Alignments grow, secondary structure prediction improves. D Przybylski B Rost, Proteins-Structure Function and Genetics 2002 46 2 197 205 10.1002/prot.10029 (Pubitemid 34052073)
12. Data classification with radial basis function networks based on a novel kernel density estimation algorithm. YJ Oyang SC Hwang YY Ou CY Chen ZW Chen, IEEE Transactions on Neural Networks 2005 16 1 225 236 10.1109/TNN.2004.836229 15732402
13. EVA. http://cubic.bioc.columbia.edu/eva/
14. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer JH Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Research 1997 25 17 3389 3402 9254694 10.1093/nar/25.17.3389 (Pubitemid 27359211)
15. CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences. WZ Li A Godzik, Bioinformatics 2006 22 13 1658 1659 10.1093/bioinformatics/btl158 16731699
16. Dictionary of Protein Secondary Structure - Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. W Kabsch C Sander, Biopolymers 1983 22 12 2577 2637 10.1002/bip.360221211 6667333
17. LIBSVM: a library for support vector machines. CC Chang CJ Lin, 2001 http://www.csie.ntu.edu.tw/∼cjlin/libsvm
18. A comparison of methods for multiclass support vector machines. CW Hsu CJ Lin, IEEE Transactions on Neural Networks 2002 13 2 415 425 10.1109/72.991427 18244442
19. Density Estimation for Statistics and Data Analysis. BW Silverman, Boca Raton: Chapman & Hall/CRC 1986
20. The Gamma Function. E Artin, New York: Holt, Rinehart and Winston 1964