Using pseudo amino acid composition to predict protein subnuclear location with improved hybrid approach

Amino Acids

Volumn 34, Issue 1, 2008, Pages 119-125

  Li, F M ^a,b   Li, Q Z ^a  

^a INNER MONGOLIA UNIVERSITY   (China)

^b INNER MONGOLIA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Chou's pseudo amino acid composition; Covariant discriminant function; Increment of diversity; Quadratic discriminant; Subnuclear localization

Indexed keywords

NUCLEAR PROTEIN;

ACCURACY; AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CELLULAR DISTRIBUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION;

ALGORITHMS; AMINO ACIDS; COMPUTATIONAL BIOLOGY; MODELS, BIOLOGICAL; PROTEINS;

EID: 38149120433     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-007-0545-9     Document Type: Article

References (72)

1. P Bell PM Lieberman GG Maul 2000 Lytic but not latent replication of Epstein-barr virus is associated with PML and induces sequential release of nuclear domain proteins J Virol 74 11800 11810
2. A Bulashevska R Eils 2006 Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains BMC Bioinformatics 7 298
3. YD Cai KC Chou 2003 Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseduo-amino acid composition Biochem Biophys Res Commun 305 407 411
4. YD Cai XJ Liu XB Xu KC Chou 2002 Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect J Cell Biochem 84 343 348
5. C Chen YX Tian XY Zou PX Cai JY Mo 2006a Using pseudo-amino acid composition and support vector machine to predict protein structural class J Theor Biol 243 444 448
6. C Chen X Zhou Y Tian X Zou P Cai 2006b Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network Anal Biochem 357 116 121
7. YL Chen QZ Li 2007 Prediction of the subcellular location of apoptosis proteins J Theor Biol 245 775 783
8. KC Chou 1995 A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space Proteins Struct Funct Genet 21 319 344
9. KC Chou 2000a Prediction of protein subcellular locations by incorporating quasi-sequence-order effect Biochem Biophys Res Commun 278 477 483
10. KC Chou 2000b Review: prediction of protein structural classes and subcellular locations Curr Protein Peptide Sci 1 171 208
11. KC Chou 2001 Prediction of protein cellular attributes using pseudo amino acid composition Proteins Struct Funct Genet 43 246 255 Erratum: ibid, 2001, Vol. 44, 60
12. KC Chou 2002 A new branch of proteomics: prediction of protein cellular attributes PW Weinrer Q Lu Gene cloning & expression technologies Eaton Publishing Westborough, MA 57 70 Chapter 4
13. KC Chou 2005 Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Bioinformatics 21 10 19
14. 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
15. KC Chou YD Cai 2003 Prediction and classification of protein subcellular location: sequence-order effect and pseudo amino acid composition J Cell Biochem 90 1250 1260 Addendum, ibid. 2004, 91, 1085
16. KC Chou YD Cai WZ Zhong 2006 Predicting networking couples for metabolic pathways of Arabidopsis EXCLI J 5 55 65
17. KC Chou DW Elrod 1998 Using discriminant function for prediction of subcellular location of prokaryotic proteins Biochem Biophys Res Commun 252 63 68
18. KC Chou D Elrod 1999 Protein subcellular location prediction Protein Eng 12 107 118
19. KC Chou GM Maggiora 1998 Domain structural class prediction Protein Eng 11 523 538
20. KC Chou HB Shen 2006a Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization Biochem Biophys Res Commun 347 150 157
21. KC Chou HB Shen 2006b Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers J Proteome Res 5 1888 1897
22. KC Chou HB Shen 2006c Large-scale predictions of Gram-negative bacterial protein subcellular locations J Proteome Res 5 3420 3428
23. KC Chou HB Shen 2006d Predicting protein subcellular location by fusing multiple classifiers J Proteome Res 99 517 527
24. KC Chou HB Shen 2007 Large-scale plant protein subcellular location prediction J Proteome Res 100 665 678
25. 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
26. KC Chou CT Zhang 1995 Review: prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275 349
27. L Cocco L Manzoli O Barnabei AM Martelli 2004 Significance of subnuclear localization of key players of inositol lipid cycle Adv Enzyme Regul 44 51 60
28. G Dellaire R Farrall WA Bickmore 2003 The nuclear protein database (NPD): subnuclear localisation and functional annotation of the nuclear proteome Nucleic Acids Res 31 328 330
29. P Du Y Li 2006 Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence BMC Bioinformatics 7 518
30. ZP Feng 2001 Prediction of the subcellular location of prokaryotic proteins based on a new representation of the amino acid composition Biopolymers 58 491 499
31. ZP Feng 2002 An overview on predicting the subcellular location of a protein In Silico Biol 2 291 303
32. QB Gao ZZ Wang C Yan YH Du 2005a Prediction of protein subcellular location using a combined feature of sequence FEBS Lett 579 3444 3448
33. Y Gao SH Shao X Xiao YS Ding YS Huang ZD Huang KC Chou 2005b Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Amino Acids 28 373 376
34. J Guo Y Lin X Liu 2006a GNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins Proteomics 6 5099 5105
35. YZ Guo M Li M Lu Z Wen K Wang G Li J Wu 2006b Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform Amino Acids 30 397 402
36. GES Heidi KM Gail N Kathryn VF Lisa F Rachel D Graham FC Javier AB Wendy 2001 Large-scale identification of mammalian proteins localized to nuclear sub-compartments Hum Mol Genet 10 1995 2011
37. Huang WL, Tung CW, Huang HL, Hwang SF, Ho SY (2007) ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physico-chemical composition features. Biosystems (DOI: 10.1016/j.biosystems. 2007.01.001)
38. K Itoh BK Brott GU Bae MJ Ratcliffe SY Sokol 2005 Nuclear localization is required for Dishevelled function in Wnt/beta-catenin signaling J Biol 4 3
39. MB Joanna AB Wendy 1998 Putting the genome on the map Trends Genet 14 403 409
40. MHM Koken A Reid F Quignon MK Chelbi-Alix JM Davies JHS Kabarowski J Zhu S Dong SJ Chen Z Chen CC Tan J Licht S Waxman H de Thé A Zelent 1997 Leukemia-associated retinoic acid receptor alpha fusion partners, PML and PLZF, heterodimerize and colocalize to nuclear bodies Proc Natl Acad Sci USA 94 10255 10260
41. RR Laxton 1978 The measure of diversity J Theor Biol 71 51 67
42. Z Lei Y Dai 2005 An SVM-based system for predicting protein subnuclear localizations BMC Bioinformatics 6 291
43. Z Lei Y Dai 2006 Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction BMC Bioinformatics 7 491
44. QZ Li ZQ Lu 2001 The prediction of the structural class of protein: application of the measure of diversity J Theor Biol 213 493 502
45. H Lin QZ Li 2007a Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components J Comput Chem 28 9 1463 1466
46. H Lin QZ Li 2007b Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant Biochem Biophys Res Commun 354 548 551
47. H Liu M Wang KC Chou 2005a Low-frequency Fourier spectrum for predicting membrane protein types Biochem Biophys Res Commun 336 737 739
48. H Liu J Yang JG Ling KC Chou 2005b Prediction of protein signal sequences and their cleavage sites by statistical rulers Biochem Biophys Res Commun 338 1005 1011
49. W Liu KC Chou 1998 Prediction of protein structural classes by modified Mahalanobis discriminant algorithm J Protein Chem 17 209 217
50. RY Luo ZP Feng JK Liu 2002 Prediction of protein structural class by amino acid and polypeptide composition Eur J Biochem 269 4219 4225
51. KL Marsh J Dixon MJ Dixon 1998 Mutations in the Treacher Collins syndrome gene lead to mislocalization of the nucleolar protein treacle Hum Mol Genet 7 1795 1800
52. S Mondal R Bhavna R Mohan Babu S Ramakumar 2006 Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification J Theor Biol 243 252 260
53. YX Pan ZZ Zhang ZM Guo GY Feng ZD Huang L He 2003 Application of pseudo amino acid composition for predicting protein subcellular location: stochastic signal processing approach J Protein Chem 22 395 402
54. RD Phair T Misteli 2000 High mobility of proteins in the mammalian cell nucleus Nature 404 604 609
55. HB Shen KC Chou 2005 Predicting protein subnuclear location with optimized evidence- theoretic K-nearest classifier and pseudo amino acid composition Biochem Biophys Res Commun 337 752 756
56. HB Shen KC Chou 2007 Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells Biopolymers 85 233 240
57. Shen HB, Yang J, Chou KC (2007) Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids (in press) (DOI: 10.1007/s00726-006-0478-8)
58. Shi JY, Zhang SW, Pan Q, Cheng YM, Xie J (2007) Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition. Amino Acids (in press) (DOI: 10.1007/s00726-006-0475-y)
59. XD Sun RB Huang 2006 Prediction of protein structural classes using support vector machines Amino Acids 30 469 475
60. G Wang RL Dunbrack Jr 2003 PISCES: a protein sequence culling server Bioinformatics 19 1589 1591
61. M Wang J Yang ZJ Xu KC Chou 2005 SLLE for predicting membrane protein types J Theor Biol 232 7 15
62. Z Wen M Li Y Li Y Guo K Wang 2007 Delaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition Amino Acids 32 277 283
63. KL Wilson MS Zastrow KK Lee 2001 Lamins and disease: insights into nuclear infrastructure Cell 104 647 650
64. X Xiao S Shao Y Ding Z Huang X Chen KC Chou 2005a An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation J Theor Biol 235 555 565
65. X Xiao S Shao Y Ding Z Huang Y Huang KC Chou 2005b Using complexity measure factor to predict protein subcellular location Amino Acids 28 57 61
66. X Xiao SH Shao YS Ding ZD Huang KC Chou 2006a Using cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49 54
67. X Xiao SH Shao ZD Huang KC Chou 2006b Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J Comput Chem 27 478 482
68. LR Zhang LF Luo 2003 Splice site prediction with quadratic discriminant analysis using diversity measure Nucleic Acids Res 31 6214 6220
69. SW Zhang Q Pan HC Zhang ZC Shao JY Shi 2006 Prediction protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and Naive Bayes feature fusion Amino Acids 30 461 468
70. GP Zhou 1998 An intriguing controversy over protein structural class prediction J Protein Chem 17 729 738
71. GP Zhou N Assa-Munt 2001 Some insights into protein structural class prediction Proteins Struct Funct Genet 44 57 59
72. GP Zhou K Doctor 2003 Subcellular location prediction of apoptosis proteins Proteins Struct Funct Genet 50 44 48