AAIndexLoc: Predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices

Amino Acids

Volumn 35, Issue 2, 2008, Pages 345-353

  Tantoso, E ^a   Li, Kuo Bin ^b  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

Amino acid indices; Subcellular localization; Support vector machine

Indexed keywords

ACCURACY; AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELLULAR DISTRIBUTION; COMPUTER PREDICTION; EXTRACTION; FUNGAL CELL; NONHUMAN; PERFORMANCE MEASUREMENT SYSTEM; PHYSICAL CHEMISTRY; PLANT CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; SENSITIVITY AND SPECIFICITY; SUPPORT VECTOR MACHINE; VALIDATION STUDY;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; INTRACELLULAR SPACE; PATTERN RECOGNITION, AUTOMATED; PREDICTIVE VALUE OF TESTS; PROTEINS;

EID: 46049118177     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-007-0616-y     Document Type: Article

References (107)

1. M Bhasin GP Raghava 2004 ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST Nucleic Acids Res 32 W414 W419
2. MP Brown WN Grundy D Lin N Cristianini CW Sugnet TS Furey M Ares Jr D Haussler 2000 Knowledge-based analysis of microarray gene expression data by using support vector machines Proc Natl Acad Sci USA 97 262 267
3. YD Cai GP Zhou KC Chou 2003 Support vector machines for predicting membrane protein types by using functional domain composition Biophys J 84 3257 3263
4. J Cedano P Aloy JA Perez-Pons E Querol 1997 Relation between amino acid composition and cellular location of proteins J Mol Biol 266 594 600
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. 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
8. YL Chen QZ Li 2007 Prediction of the subcellular location of apoptosis proteins J Theor Biol 245 775 783
9. KC Chou 2000a Prediction of protein structural classes and subcellular locations Curr Protein Pept Sci 1 171 208
10. KC Chou 2000b Prediction of protein subcellular locations by incorporating quasi-sequence-order effect Biochem Biophys Res Commun 278 477 483
11. KC Chou 2000c Review: prediction of protein structural classes and subcellular locations Curr Protein Peptide Sci 1 171 208
12. KC Chou 2001 Prediction of protein cellular attributes using pseudo-amino acid composition Proteins 43 246 255
13. KC Chou 2002 A new branch of proteomics: prediction of protein cellular attributes PW Weinrer Q Lu Gene cloning and expression technologies Eaton Publishing Westborough MA 57 70
14. KC Chou 2005 Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Bioinformatics 21 10 19
15. 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
16. KC Chou YD Cai 2003 A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology Biochem Biophys Res Commun 311 743 747
17. KC Chou YD Cai 2005 Prediction of membrane protein types by incorporating amphipathic effects J Chem Inf Model 45 407 413
18. KC Chou DW Elrod 1998 Using discriminant function for prediction of subcellular location of prokaryotic proteins Biochem Biophys Res Commun 252 63 68
19. KC Chou DW Elrod 1999a Prediction of membrane protein types and subcellular locations Proteins 34 137 153
20. KC Chou DW Elrod 1999b Protein subcellular location prediction Protein Eng 12 107 118
21. KC Chou HB Shen 2006a Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization Biochem Biophys Res Commun 347 150 157
22. 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
23. KC Chou HB Shen 2006c Predicting protein subcellular location by fusing multiple classifiers J Cell Biochem 99 517 527
24. KC Chou HB Shen 2007a Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites J Proteome Res 6 1728 1734
25. KC Chou HB Shen 2007b Large-scale plant protein subcellular location prediction J Cell Biochem 100 665 678
26. KC Chou HB Shen 2007c 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
27. KC Chou HB Shen 2007d Recent progress in protein subcellular location prediction Anal Biochem 370 1 16
28. KC Chou HB Shen 2007e Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides Biochem Biophys Res Commun 357 633 640
29. 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
30. KC Chou CT Zhang 1995 Prediction of protein structural classes Crit Rev Biochem Mol Biol 30 275 349
31. S Clausmeyer RB Klosgen RG Herrmann 1993 Protein import into chloroplasts. The hydrophilic lumenal proteins exhibit unexpected import and sorting specificities in spite of structurally conserved transit peptides J Biol Chem 268 13869 13876
32. 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
33. 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
34. O Emanuelsson H Nielsen S Brunak G von Heijne 2000 Predicting subcellular localization of proteins based on their N-terminal amino acid sequence J Mol Biol 300 1005 1016
35. T Endo I Shimada D Roise F Inagaki 1989 N-terminal half of a mitochondrial presequence peptide takes a helical conformation when bound to dodecylphosphocholine micelles: a proton nuclear magnetic resonance study J Biochem (Tokyo) 106 396 400
36. 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
37. ZP Feng 2002 An overview on predicting the subcellular location of a protein In Silico Biol 2 291 303
38. ZP Feng CT Zhang 2001 Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids Int J Biol Macromol 28 255 261
39. 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
40. Y Gao S Shao X Xiao Y Ding Y Huang Z 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
41. JL Gardy C Spencer K Wang M Ester GE Tusnady I Simon S Hua K deFays C Lambert K Nakai FS Brinkman 2003 PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria Nucleic Acids Res 31 3613 3617
42. A Garg M Bhasin GP Raghava 2005 Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search J Biol Chem 280 14427 14432
43. 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
44. 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
45. PK Hammen DG Gorenstein H Weiner 1994 Structure of the signal sequences for two mitochondrial matrix proteins that are not proteolytically processed upon import Biochemistry 33 8610 8617
46. A Hoglund P Donnes T Blum HW Adolph O Kohlbacher 2006 MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid composition Bioinformatics 22 1158 1165
47. S Hua Z Sun 2001 Support vector machine approach for protein subcellular localization prediction Bioinformatics 17 721 728
48. Y Huang Y Li 2004 Prediction of protein subcellular locations using fuzzy k-NN method Bioinformatics 20 21 28
49. L Jin H Tang W Fang 2005 Prediction of protein subcellular locations using a new measure of information discrepancy J Bioinform Comput Biol 3 915 927
50. KD Kedarisetti L Kurgan S Dick 2006 Classifier ensembles for protein structural class prediction with varying homology Biochem Biophys Res Commun 348 981 988
51. K Keegstra K Cline 1999 Protein import and routing systems of chloroplasts Plant Cell 11 557 570
52. EW Klee JA Finlay C McDonald JR Attewell D Hebrink R Dyer B Love G Vasmatzis TM Li JM Beechem GG Klee 2006 Bioinformatics methods prioritizing serum biomarker candidates J Clin Chem 52 2162 2164
53. LA Kurgan W Stach J Ruan 2007 Novel scales based on hydrophobicity indices for secondary protein structure J Theor Biol 248 354 366
54. K Lee DW Kim D Na KH Lee D Lee 2006 PLPD: reliable protein localization prediction from imbalanced and overlapped datasets Nucleic Acids Res 34 4655 4666
55. Y Lee CK Lee 2003 Classification of multiple cancer types by multicategory support vector machines using gene expression data Bioinformatics 19 1132 1139
56. Z Lei Y Dai 2005 An SVM-based system for predicting protein subnuclear localizations BMC Bioinformatics 6 291
57. H Lin QZ Li 2007a Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant Biochem Biophys Res Commun 354 548 551
58. H Lin QZ Li 2007b Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components J Comput Chem 28 1463 1466
59. 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
60. H Liu M Wang KC Chou 2005a Low-frequency Fourier spectrum for predicting membrane protein types Biochem Biophys Res Commun 336 737 739
61. H Liu J Yang M Wang L Xue KC Chou 2005b Using fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types Protein J 24 385 389
62. M Mahdavi Y-H Lin 2007 False positive reduction in protein-protein interaction predictions using gene ontology annotations BMC Bioinformatics 8 262
63. S Matsuda JP Vert H Saigo N Ueda H Toh T Akutsu 2005 A novel representation of protein sequences for prediction of subcellular location using support vector machines Protein Sci 14 2804 2813
64. BW Matthews 1975 Comparison of the predicted and observed secondary structure of T4 phage lysozyme Biochim Biophys Acta 405 442 451
65. 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
66. 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 Recogn Lett 28 1610 1615
67. RF Murphy MV Boland M Velliste 2000 Towards a systematics for protein subcelluar location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images Proc Int Conf Intell Syst Mol Biol 8 251 259
68. K Nakai 2000 Protein sorting signals and prediction of subcellular localization Adv Protein Chem 54 277 344
69. K Nakai P Horton 1999 PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization Trends Biochem Sci 24 34 36
70. K Nakai M Kanehisa 1992 A knowledge base for predicting protein localization sites in eukaryotic cells Genomics 14 897 911
71. H Nakashima K Nishikawa 1994 Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies J Mol Biol 238 54 61
72. B Niu YD Cai WC Lu GZ Li KC Chou 2006 Predicting protein structural class with AdaBoost Learner Protein Pept Lett 13 489 492
73. 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
74. KJ Park M Kanehisa 2003 Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs Bioinformatics 19 1656 1663
75. 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
76. A Reinhardt T Hubbard 1998 Using neural networks for prediction of the subcellular location of proteins Nucleic Acids Res 26 2230 2236
77. D Sarda GH Chua KB Li A Krishnan 2005 pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties BMC Bioinformatics 6 152
78. H Shen KC Chou 2005a 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
79. HB Shen KC Chou 2005b Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition Biochem Biophys Res Commun 337 752 756
80. HB Shen KC Chou 2006 Ensemble classifier for protein fold pattern recognition Bioinformatics 22 1717 1722
81. HB Shen KC Chou 2007a Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Protein Eng Des Sel 20 39 46
82. HB Shen KC Chou 2007b 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
83. HB Shen KC Chou 2007c Using ensemble classifier to identify membrane protein types Amino Acids 32 483 488
84. HB Shen KC Chou 2007d Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells Biopolymers 85 233 240
85. 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
86. 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
87. JY Shi SW Zhang Q Pan YM 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
88. XD Sun RB Huang 2006 Prediction of protein structural classes using support vector machines Amino Acids 30 469 475
89. V Vapnik 1995 The nature of statistical learning theory Springer-Verlag New York
90. 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
91. 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
92. 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
93. JJ Ward LJ McGuffin BF Buxton DT Jones 2003 Secondary structure prediction with support vector machines Bioinformatics 19 1650 1655
94. 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
95. X Xiao S Shao Y Ding Z Huang KC Chou 2006a Using cellular automata images and pseudo amino acid composition to predict protein subcellular location Amino Acids 30 49 54
96. 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
97. 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
98. D Xie A Li M Wang Z Fan H Feng 2005 LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST Nucleic Acids Res 33 W105 W110
99. CS Yu CJ Lin JK Hwang 2004 Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions Protein Sci 13 1402 1406
100. Z Yuan 1999 Prediction of protein subcellular locations using Markov chain models FEBS Lett 451 23 26
101. SW Zhang Q Pan HC Zhang ZC Shao JY Shi 2006a Prediction of 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
102. T Zhang Y Ding KC Chou 2006b Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence Comput Biol Chem 30 367 371
103. TL Zhang YS Ding 2007 Using pseudo amino acid composition and binary-tree support vector machines to predict protein structural classes Amino Acids 33 623 629
104. GP Zhou 1998 An intriguing controversy over protein structural class prediction J Protein Chem 17 729 738
105. GP Zhou N Assa-Munt 2001 Some insights into protein structural class prediction Proteins 44 57 59
106. GP Zhou K Doctor 2003 Subcellular location prediction of apoptosis proteins Proteins 50 44 48
107. 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