Prediction of protein structural classes using support vector machines

Amino Acids

Volumn 30, Issue 4, 2006, Pages 469-475

  Sun, X D ^a   Huang, R B ^a  

^a GUANGXI UNIVERSITY   (China)

Author keywords

CATH; Jackknifing; Multi class; Protein structural class prediction; Support vector machines

Indexed keywords

DIPEPTIDE; PROTEIN SUBUNIT; TRIPEPTIDE;

ACCURACY; ALPHA HELIX; ANALYTIC METHOD; ARTICLE; BETA SHEET; MACHINE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN QUATERNARY STRUCTURE; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATABASES, FACTUAL; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 33745093400     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-005-0239-0     Document Type: Article

References (65)

1. P Aloy R Russell 2004 Ten thousand interactions for the molecular biologist Nature Biotechnol 22 1317 1321
2. CB Anfinsen 1973 Principles that govern folding of protein chain Science 181 223
3. Anguita D, Ridella S, Sterpi D (2004) A new method for multiclass support vector machines. In: Neural Networks, 2004. Proceedings 2004 IEEE International Joint Conference, pp 412-417
4. HM Berman T Battistuz TN Bhat WF Bluhm PE Bourne K Burkhardt 2002 The protein data bank Acta Cryst D 58 899 907
5. C Branden J Tooze 1999 Introduction to protein structure 2 Garland Publishing New York
6. MPS Brown WN Grundy D Lin N Cristianini CW Sugnet TS Furey 2000 Knowledge-based analysis of microarray gene expression data by using support vector machine Proc Natl Acad Sci USA 97 262 267
7. YD Cai XJ Liu XB Xu KC Chou 2000 Support vector machines for prediction of subcellular location Mol Cell Biol Res Commun 4 230 233
8. YD Cai XJ Liu XB Xu KC Chou 2002a Support vector machines for predicting the specificity of GalNAc-transferase Peptides 23 205 208
9. YD Cai XJ Liu XB Xu KC Chou 2002b Prediction of protein structure classes by support vector machines Comput Chem 26 293 296
10. YD Cai XJ Liu YX Li XB Xu KC Chou 2003a Prediction of β-turns with learning machines Peptides 24 665 659
11. YD Cai XJ Liu JB Xu KC Chou 2003b Support vector machines for prediction of protein domain structural class J Theor Biol 221 115 120
12. JM Chandonia M Karplus 1995 Neural networks for secondary structure and structural class prediction Protein Sci 4 275 285
13. Chang C-C, Lin C-J (2001) LIBSVM: a library for support vector machines. Software available at: http://www.csie.ntu.edu.tw/∼cjlin/libsvm
14. E Chargaff 1951 Structure and function of nucleic acids as cell constituents Fed Proc 10 654 659
15. E Chargaff 1979 How genetics got a chemical education Ann NY Acad Sci 325 345 360
16. C Chothia 1992 One thousand families for the molecular biologist Nature 357 543 544
17. JJ Chou CT Zhang 1993 A joint prediction of the folding types of 1490 human proteins from their genetic codons J Theor Biol 161 251 262
18. KC Chou 1995 A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space Proteins 21 319 344
19. KC Chou 2000 Review: Prediction of protein structural classes and subcellular locations Curr Protein Pept Sci 1 171 208
20. KC Chou YD Cai 2002 Using functional domain composition and support vector machines for prediction of protein subcellular location J Biol Chem 277 45765 45769
21. KC Chou YD Cai 2004 Predicting protein structural class by functional domain composition Biochem Biophys Res Comm 321 1007 1009
22. KC Chou DW Elrod 1998 Using discriminant function for prediction of subcellular location of prokaryotic proteins Biochem Biophys Res Commun 252 63 68
23. KC Chou DW Elrod 1999a Protein subcellular location prediction Protein Eng 12 107 118
24. KC Chou DW Elrod 1999b Prediction of membrane protein types and subcellular locations Proteins 34 137 153
25. KC Chou GM Maggiora 1998 Domain structural class prediction Protein Eng 11 523 538
26. KC Chou W Liu GM Maggiora CT Zhang 1998 Prediction and classification of domain structural classes Proteins 31 97 103
27. KC Chou CT Zhang 1994 Predicting protein folding types by distance functions that make allowances for amino acid interactions J Biol Chem 269 22014 22020
28. KC Chou CT Zhang 1995 Review: Prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275 349
29. Chou PY (1980) Amino acid composition of four classes of proteins. In: Abstracts of Papers, Part I, Second Chemical Congress of the North American Continent, Las Vegas, Nevada
30. PY Chou 1989 Prediction of protein structural classes from amino acid composition GD Fasman Prediction of protein structure and the principles of protein conformation Plenum Press New York 549 586
31. T Creighton 1993 Proteins, structures and molecular properties 2 Freeman and Company New York
32. N Cristianini J Shawe-Taylor 2000 An introduction to support vector machines Cambridge University Press Cambridge
33. CHQ Ding I Dubchak 2001 Multi-class protein fold recognition using support vector machines and neural networks Bioinformatics 17 345 358
34. I Dubchak SR Holbrook SH Kim 1993 Predicting protein secondary structure content: a tandem neural network approach Proteins 16 79 91
35. QS Du DQ Wei KC Chou 2003 Correlations of amino acids in protein Peptides 24 1863 1869
36. S Hua S Sun 2001 A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach J Mol Biol 302 397 407
37. TJP Hubbard J Park 1995 Fold recognition and ab initio structure predictions using Hidden Markov Models and b-strand pair potentials Proteins 23 398 402
38. Z Isik B Yanikoglu U Sezerman 2004 Protein structural class determination using support vector machines C Aykanat T Dayar I Korpeoglu Lecture notes in computer science Computer and information sciences 3280 Springer New York 82 89
39. V Kecman 2001 Learning and soft computing MIT Press Cambridge
40. P Klein C Delisi 1986 Prediction of protein structural class from amino acid sequence Biopolymers 25 1659 1672
41. Leslie C, Eskim E, Noble SW (2002) The spectrum kernel: a string kernel for SVM protein classification. In: Proc. Pacific Symposium on Biocomputing 7: 566-775
42. M Levitt C Chothia 1976 Structural patterns in globular proteins Nature 261 552 558
43. RY Luo ZP Feng JK Liu 2002 Prediction of protein structural class by amino acid and polypeptide composition Eur J Biochem 269 4219 4225
44. F Markowetz L Edler M Vingron 2003 Support vector machines for protein fold class prediction Biometr J 45 377 389
45. BA Metfessel PN Saurugger DP Connelly ST Rich 1993 Cross-validation of protein structural class prediction using statistical clustering and neural networks Protein Sci 2 1171 1182
46. H Nakashima K Nishikawa T Ooi 1986 The folding type of a protein is relevant to the amino acid composition J Biochem 99 152 162
47. MN Nguyen JC Rajapakse 2003 Multi-class support vector machines for protein secondary structure prediction Genome Informatics 14 218 227
48. CA Orengo AD Machie S Jones DT Jones MB Swindells SM Thornton 1997 CATH - a hierarchic classification of protein domain structures Structure 5 1093 1108
49. JC Platt 1999 Fast training of support vector machines using sequsntial minimal optimization B Scholkopf CJC Verges AJ Smola Advances in kernel methods: support vector learning MIT Press Cambridge
50. JS Rechardson DC Rechardson 1989 Principles and patterns of protein conformation GD Fasman Prediction of protein structure and the principles of protein conformation Plenum Press New York 1 98
51. B Rost C Sander 1993 Prediction of protein secondary structure at better than 70% accuracy J Mol Biol 232 584 599
52. B Rost C Sander 1994 Combining evolutionary information and neural networks to predict protein secondary structure Proteins 19 55 72
53. S Saxonon W Gilbert 2003 The universal of exons revisited Genetica 118 267 278
54. B Scholkopf A Smola 2002 Learning with kernels MIT Press Cambridge
55. M Sela FH White Jr CB Anfinsen 1957 Reductive cleavage of disulfide bridges in ribonuclease Science 125 691 692
56. N Sueoka 1961 Compositional correlations between deoxyribonucleic acid and protein Cold Spring Hard Symp Quant Biol 26 35 43
57. WR Taylor CA Orengo 1989 Protein structure alignment J Mol Biol 208 1 22
58. J Thorsten 2002 Learning to classify text using support vector machines Kluwer Norwell
59. V Vapnik 1995 Statistical learning theory Wiley New York
60. ZR Yang 2004 Biological applications of support vector machines Brief Bioinformatics 5 328 338
61. ZR Yang KC Chou 2004 Bio-support vector machines for computational proteomic Bioinformatics 20 735 741
62. CT Zhang KC Chou 1992 An optimization approach to predicting protein structural class from amino acid composition Protein Sci 1 401 408
63. GP Zhou 1998 An intriguing controversy over protein structural class prediction J Protein Chem 17 729 738
64. GP Zhou N Assa-Munt 2001 Some insights into protein structural class prediction Proteins Struct Funct Genet 44 57 59
65. GP Zhou K Doctor 2003 Subcellular location prediction of apoptosis proteins Proteins Struct Funct Genet 50 44 48