An ensemble of reduced alphabets with protein encoding based on grouped weight for predicting DNA-binding proteins

Amino Acids

Volumn 36, Issue 2, 2009, Pages 167-175

  Nanni, Loris ^a   Lumini, Alessandra ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Amino acid alphabets; DNA binding proteins; Ensemble classifier; Multi classifier; Support vector machine

Indexed keywords

AMINO ACID; DNA BINDING PROTEIN; PROTEINASE;

ACCURACY; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLASSIFIER; CORRELATION COEFFICIENT; DNA EXTRACTION; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; SUPPORT VECTOR MACHINE;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DNA-BINDING PROTEINS; MODELS, CHEMICAL; SEQUENCE ANALYSIS, PROTEIN;

EID: 59449107736     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-008-0044-7     Document Type: Article

References (100)

1. G Aguero-Chapin H Gonzalez-Diaz R Molina J Varona-Santos E Uriarte Y Gonzalez-Diaz 2006 Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L FEBS Lett 580 723 730
2. S Ahmad A Sarai 2005 PSSM-based prediction of DNA binding sites in proteins BMC Bioinformatics 6 33
3. S Ahmad MM Gromiha A Sarai 2004 Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information Bioinformatics 20 477 486
4. N Bhardwaj RE Langlois G Zhao H Lu 2005 Kernel-based machine learning protocol for predicting DNA-binding proteins Nucleic Acids Res 33 6486 6493
5. J Caballero L Fernandez M Garriga JI Abreu S Collina M Fernandez 2007 Proteometric study of ghrelin receptor function variations upon mutations using amino acid sequence autocorrelation vectors and genetic algorithm-based least square support vector machines J Mol Graph Model 26 166 178
6. YD Cai KC Chou 2006 Predicting membrane protein type by functional domain composition and pseudo amino acid composition J Theor Biol 238 395 400
7. YL Chen QZ Li 2007 Prediction of apoptosis protein subcellular location using improved hybrid approach and pseudo amino acid composition J Theor Biol 248 377 381
8. YL Chen QZ Li 2007 Prediction of the subcellular location of apoptosis proteins J Theor Biol 245 775 783
9. C Chen YX Tian XY Zou PX Cai JY Mo 2006 Using pseudo-amino acid composition and support vector machine to predict protein structural class J Theor Biol 243 444 448
10. C Chen X Zhou Y Tian X Zou P Cai 2006 Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network Anal Biochem 357 116 121
11. J Chen H Liu J Yang KC Chou 2007 Prediction of linear B-cell epitopes using amino acid pair antigenicity scale Amino Acids 33 423 428
12. KC Chou 2000 Prediction of protein subcellular locations by incorporating quasi-sequence-order effect Biochem Biophys Res Commun 278 477 483
13. KC Chou 2001 Prediction of protein cellular attributes using pseudo amino acid composition Proteins 43 246 255 (Erratum: ibid, 2001, 44:60)
14. KC Chou 2005 Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Bioinformatics 21 10 19
15. KC Chou HB Shen 2006 Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization Biochem Biophys Res Commun 347 150 157
16. KC Chou HB Shen 2006 Large-scale predictions of Gram-negative bacterial protein subcellular locations J Proteome Res 5 3420 3428
17. KC Chou HB Shen 2007 Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites J Proteome Res 6 1728 1734
18. KC Chou HB Shen 2007 Large-scale plant protein subcellular location prediction J Cell Biochem 100 665 678
19. KC Chou HB Shen 2007 MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM Biochem Biophys Res Commun 360 339 345
20. KC Chou HB Shen 2007 Review: recent progresses in protein subcellular location prediction Anal Biochem 370 1 16
21. KC Chou HB Shen 2007 Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides Biochem Biophys Res Commun 357 633 640
22. KC Chou HB Shen 2008 Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms Nat Protoc 3 153 162
23. KC Chou CT Zhang 1995 Review: prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275 349
24. Cristianini N, Shawe-Taylor J (2000) An introduction to support vector machines and other kernel-based learning methods. Cambridge University Press, London
25. Y Diao M Li Z Feng J Yin Y Pan 2007 The community structure of human cellular signaling network J Theor Biol 247 608 615
26. Y Diao D Ma Z Wen J Yin J Xiang M Li 2008 Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Amino Acids 34 1 111 117 10.1007/s00726-007-0550-z
27. YS Ding TL Zhang KC Chou 2007 Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network Protein Pept Lett 14 811 815
28. 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
29. Duda RO, Hart PE, Stork G (2000) Pattern classification, 2nd edn. Wiley, New York
30. Y Fang Y Guo Y Feng M Li 2008 Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features Amino Acids 34 1 103 109 10.1007/s00726-007-0568-2
31. Fawcett T (2004) ROC graphs: notes and practical considerations for researchers. HP Laboratories, technical report, Palo Alto
32. ZP Feng 2002 An overview on predicting the subcellular location of a protein In Silico Biol 2 291 303
33. Y Gao SH Shao X Xiao YS Ding YS Huang ZD Huang KC Chou 2005 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. H Gonzalez-Diaz A Perez-Bello E Uriarte Y Gonzalez-Diaz 2006 QSAR study for mycobacterial promoters with low sequence homology Bioorg Med Chem Lett 16 547 553
35. H Gonzalez-Diaz G Aguero-Chapin J Varona R Molina G Delogu L Santana E Uriarte G Podda 2007 2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function J Comput Chem 28 1049 1056
36. H Gonzalez-Diaz Y Perez-Castillo G Podda E Uriarte 2007 Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices J Comput Chem 28 1990 1995
37. H Gonzalez-Diaz S Vilar L Santana E Uriarte 2007 Medicinal chemistry and Bioinformatics - current trends in drugs discovery with networks topological indices Curr Top Med Chem 10 1015 1029
38. YZ Guo M Li M Lu Z Wen K Wang G Li J Wu 2006 Classifying G protein-coupled receptors and nuclear receptors based on protein power spectrum from fast Fourier transform Amino Acids 30 397 402
39. S Hwang Z Gou IB Kuznetsov 2007 DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins Bioinformatics 23 5 634 636
40. S Jones HP Shanahan HM Berman JM Thornton 2003 Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins Nucleic Acids Res 31 7189 7198
41. KD Kedarisetti LA Kurgan S Dick 2006 Classifier ensembles for protein structural class prediction with varying homology Biochem Biophys Res Commun 348 981 988
42. M Keil TE Exner J Brickmann 2004 Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network J Comput Chem 25 779 789
43. J Kittler M Hatef R Duin J Matas 1998 On combining classifiers IEEE Trans Pattern Anal Mach Intell 3 226 239
44. LA Kurgan W Stach J Ruan 2007 Novel scales based on hydrophobicity indices for secondary protein structure J Theor Biol 248 354 366
45. IB Kuznetsov Z Gou R Li S Hwang 2006 Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins Proteins 64 19 27
46. ES Lander LM Linton B Birren C Nusbaum MC Zody J Baldwin K Devon K Dewar M Doyle W FitzHugh 2001 Initial sequencing and analysis of the human genome Nature 409 860 921
47. FM Li QZ Li 2007 Using pseudo amino acid composition to predict protein subnuclear location with improved hybrid approach Amino Acids 34 119 125
48. H Lin QZ Li 2007 Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant Biochem Biophys Res Commun 354 548 551
49. H Lin QZ Li 2007 Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components J Comput Chem 28 1463 1466
50. H Liu M Wang KC Chou 2005 Low-frequency Fourier spectrum for predicting membrane protein types Biochem Biophys Res Commun 336 737 739
51. H Liu J Yang M Wang L Xue KC Chou 2005 Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types Protein J 24 385 389
52. DQ Liu H Liu HB Shen J Yang KC Chou 2007 Predicting secretory protein signal sequence cleavage sites by fusing the marks of global alignments Amino Acids 32 493 496
53. 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
54. P Mundra M Kumar KK Kumar VK Jayaraman BD Kulkarni 2007 Using pseudo amino acid composition to predict protein subnuclear localization: approached with PSSM Pattern Recognit Lett 28 1610 1615
55. L Nanni A Lumini 2006 An ensemble of K-local hyperplane for predicting protein-protein interactions Bioinformatics 22 1207 1210
56. L Nanni A Lumini 2006 MppS: an ensemble of support vector machine based on multiple physicochemical properties of amino-acids Neurocomputing 69 1688 1690
57. L Nanni A Lumini 2008 A genetic approach for building different alphabets for peptide and protein classification BMC Bioinformatics 9 45
58. Nanni L, Lumini A (2008b) Combing ontologies and dipeptide composition for predicting DNA-binding proteins. Amino Acids. doi: 10.1007/s00726-007-0016-3
59. B Niu YD Cai WC Lu GY Zheng KC Chou 2006 Predicting protein structural class with AdaBoost learner Protein Pept Lett 13 489 492
60. Y Ofran V Mysore B Rost 2007 Prediction of DNA-binding residues from sequence Bioinformatics 23 13 347 353
61. 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
62. X Pu J Guo H Leung Y Lin 2007 Prediction of membrane protein types from sequences and position-specific scoring matrices J Theor Biol 247 259 265
63. SK Riis A Krogh 1996 Improving prediction of protein secondary structure using neural networks and multiple sequence alignments J Comput Biol 3 163 183
64. HP Shanahan MA Garcia S Jones JM Thornton 2004 Identifying DNA-binding proteins using structural motifs and the electrostatic potential Nucleic Acids Res 32 4732 4741
65. 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
66. HB Shen KC Chou 2005 Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo amino acid composition to predict membrane protein types Biochem Biophys Res Commun 334 288 292
67. HB Shen KC Chou 2006 Ensemble classifier for protein fold pattern recognition Bioinformatics 22 1717 1722
68. HB Shen KC Chou 2007 EzyPred: a top-down approach for predicting enzyme functional classes and subclasses Biochem Biophys Res Commun 364 53 59
69. HB Shen KC Chou 2007 Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Protein Eng Des Sel 20 39 46
70. HB Shen KC Chou 2007 Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites Biochem Biophys Res Commun 355 1006 1011
71. HB Shen KC Chou 2007 Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM Protein Eng Des Sel 20 561 567
72. HB Shen KC Chou 2007 PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition Anal Biochem 373 386 388
73. HB Shen KC Chou 2007 Signal-3L: a 3-layer approach for predicting signal peptide Biochem Biophys Res Commun 363 297 303
74. HB Shen KC Chou 2007 Using ensemble classifier to identify membrane protein types Amino Acids 32 483 488
75. 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
76. HB Shen J Yang KC Chou 2006 Fuzzy KNN for predicting membrane protein types from pseudo amino acid composition J Theor Biol 240 9 13
77. HB Shen J Yang KC Chou 2007 Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction Amino Acids 33 57 67
78. JY Shi SW Zhang Q Pan Y-M Cheng J Xie 2007 Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition Amino Acids 33 69 74
79. XD Sun RB Huang 2006 Prediction of protein structural classes using support vector machines Amino Acids 30 469 475
80. F Tan X Feng Z Fang M Li Y Guo L Jiang 2007 Prediction of mitochondrial proteins based on genetic algorithm - partial least squares and support vector machine Amino Acids 33 669 675
81. Y Tsuchiya K Kinoshita H Nakamura 2004 Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces Proteins 55 885 894
82. C Yan M Terribilini F Wu RL Jernigan D Dobbs V Honavar 2006 Predicting DNA-binding sites of proteins from amino acid sequence BMC Bioinformatics 7 262
83. L Wang SJ Brown 2006 Prediction of DNA-binding residues from sequence features J Bioinform Comput Biol 4 6 1141 1158
84. M Wang J Yang GP Liu ZJ Xu KC Chou 2004 Weighted-support vector machines for predicting membrane protein types based on pseudo amino acid composition Protein Eng Des Sel 17 509 516
85. M Wang J Yang KC Chou 2005 Using string kernel to predict signal peptide cleavage site based on subsite coupling model Amino Acids 28 395 402 (Erratum: ibid, 2005, 29:301)
86. SQ Wang J Yang KC Chou 2006 Using stacked generalization to predict membrane protein types based on pseudo amino acid composition J Theor Biol 242 941 946
87. Z Wen M Li Y Li Y Guo K Wang 2006 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
88. X Xiao KC Chou 2007 Digital coding of amino acids based on hydrophobic index Protein Pept Lett 14 871 875
89. X Xiao S Shao Y Ding Z Huang X Chen KC Chou 2005 Using cellular automata to generate image representation for biological sequences Amino Acids 28 29 35
90. X Xiao S Shao Y Ding Z Huang Y Huang KC Chou 2005 Using complexity measure factor to predict protein subcellular location Amino Acids 28 57 61
91. X Xiao SH Shao YS Ding ZD Huang KC Chou 2006 Using cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49 54
92. X Xiao SH Shao ZD Huang KC Chou 2006 Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J Comput Chem 27 478 482
93. TL Zhang YS Ding 2007 Using pseudo amino acid composition and binary-tree support vector machines to predict protein structural classes Amino Acids 33 4 623 629 10.1007/s00726-007-0496-1
94. 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
95. T Zhang Y Ding KC Chou 2006 Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence Comput Biol Chem 30 367 371
96. Z-H Zhang Z-H Wang Z-R Zhang Y-X Wang 2006 A novel method for apoptosis protein subcellular localization prediction combining encoding based on grouped weight and support vector machine FEBS Lett 580 6169 6174
97. Zhang SW, Zhang YL, Yang HF, Zhao CH, Pan Q (2007) Using the concept of Chou's pseudo amino acid composition to predict protein subcellular localization: an approach by incorporating evolutionary information and von Neumann entropies. Amino Acids. doi: 10.1007/s00726-007-0010-9
98. GP Zhou 1998 An intriguing controversy over protein structural class prediction J Protein Chem 17 729 738
99. GP Zhou K Doctor 2003 Subcellular location prediction of apoptosis proteins Proteins 50 44 48
100. XB Zhou C Chen ZC Li XY Zou 2007 Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes J Theor Biol 248 546 551