Protein subcellular localization based on PSI-BLAST and machine learning

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 6, 2006, Pages 1181-1195

  Guo, Jian ^a   Pu, Xian ^b   Lin, Yuanlie ^a   Leung, Howard ^b  

^a TSINGHUA UNIVERSITY   (China)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Multiple sequence alignment; Position specific scoring matrix; Probabillstic neural network; PSI BLAST; Subcellular localization

Indexed keywords

AMINO ACID;

ACCURACY; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; ARTIFICIAL NEURAL NETWORK; CELLULAR DISTRIBUTION; CLASSIFIER; CONTROLLED STUDY; INTERMETHOD COMPARISON; MACHINE LEARNING; NONHUMAN; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN LOCALIZATION; PSI-BLAST; QUALITY CONTROL; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS;

ARTIFICIAL INTELLIGENCE; DATABASES, PROTEIN; PATTERN RECOGNITION, AUTOMATED; PROTEOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; SUBCELLULAR FRACTIONS;

EID: 33846488101     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006002405     Document Type: Article

References (58)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res 25:3389-3402, 1997.
2. Bhasin M, Garg A, Raghava GPS, PSLpred: Prediction of subcellular localization of bacterial proteins, Bioinformatics 21(10):2522-2524, 2005.
3. Bhasin M, Raghava, GPS, ESLpred: SVM based method for subcellular localization of eukaryotic proteins using dipeptide composition and psi-blast, Nucleic Acids Res 32(Webserver Issue):414-419, 2004.
4. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M, The SWISSPROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365-37, 2003.
5. Cai YD, Chou KC, Predicting subcellular localization of proteins in a hybridization space, Bioinformatics 20:1151-1156, 2004.
6. Cai YD, Chou KC, Predicting membrane protein type by functional domain composition and pseudo amino acid composition, J Theor Biol 238:395-400, 2006.
7. Cedano J, Aloy P, Perez-Pons JA, Querol E, Relation between amino acid composition and cellular location of proteins, J Mol Boil 266:594-600, 1997.
8. Chou KC, Prediction of protein subcellular locations by incorporating quasi-sequenceoder effect, Biochem Biophys Res Commun 278:477-483, 2000.
9. Chou KC, Review: Prediction of protein structural classes and subcellular locations, Curr Protein Peptide Sci 1:171-208, 2000.
10. Chou KC, Prediction of protein cellular attributes using pseudo amino acid composition, PROTEINS: Structure, Function, and Genetics 43:246-255, 2001.
11. Chou KC, Cai YD, Using functional domain composition and support vector machines for prediction of protein subcellular location, J Biol Chem 277:45765-45769, 2002.
12. Chou KC, Cai YD, A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology, Biochem, Biophys Res Commun 311:743-747, 2003.
13. Chou KC, Cai YD, Prediction and classification of protein subcellular location: Sequence-order effect and pseudo amino acid composition, J Cell Biochem 90:1250-1260, 2003.
14. Chou KC, Cal YD, Prediction of protein subcellular locations by GO-FunD-PseAA predicor, Biochem Biophys Res Commun 320:1236-1239, 2004.
15. Chou KC, Cai YD, Predicting protein localization in budding yeast, Bioinformatics 21:944-950, 2005.
16. Chou KC, Cai YD, Using GO-PseAA predictor to identify membrane proteins and their types, Biochem Biophys Res Commun 327:845-847, 2005.
17. Chou KC, Elord DW, Using discriminant function for prediction of subcellular location of prokaryotic proteins, Biochem Biophys Res Commun 252:63-68, 1998.
18. Chou KC, Elord DW, Protein subcellular location prediction, Protein Eng 12:107-118, 1999.
19. Chou KC, Shen HB, Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization, Biochem Biophys Res Commun 347:150-157, 2006.
20. Chou KC, Zhang CT, Review: Prediction of protein structural classes, Crit Rev Biochem Mol Biol 30:275-349, 1995.
21. Emanuelsson O, Nielsen H, Brunak S, von Heijne G, Predicting subcellular localization of proteins based on their N-terminal amino acid sequence, J Mol Biol 300:1005-1016, 1997.
22. Feng Z, Prediction of the subcellular location of prokaryotic proteins based on a new representation of the amino acid composition, Biopolymers 58:491-499, 2001.
23. Feng Z, An overview on predicting the subcellular location of a protein, In Silico Biol 2:291-303, 2002.
24. Gao Y, Shao SH, Xiao X, Ding YS, Huang YS, Huang ZD, Chou KC, Using pseudo amino acid composition to predict protein subcellular location: Approached with lyapunov index, bessel function, and chebyshev filter, Amino Acids 28:373-376, 2005.
25. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FSL, PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics 21(5):617-623, 2005.
26. Gardy JL, Spencer C, Wang K, Ester M, Tusnady GE, Simon I, Hua SJ, deFays K, Lambert C, Nakai K, Brinkman FSL, PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria, Nucleic Acids Res 31(13): 3613-3617, 2003.
27. Garg A, Bhasin M, Raghava GPS, SVM-based method for subcellular localization of human proteins using amino acid compositions, their order and similarity search, J Biol Chem 280:14427-14432, 2005.
28. Guo J, Lin YL, Sun ZR, A novel method for protein subcellular localization: Combining residue-couple model and SVM, Proc APBC 2005, pp. 117-129, 2005.
29. Guo YZ, Li M, Lu M, Wen Z, Wang K, Li G, Wu J, Classifying G protein-coupled receptors and nuclear receptors based on protein power spectrum from fast fourier transform, Amino Acids; DOI: 10.1007/ S00726-006-0332-z, 2006.
30. Hirokawa T, Boon-Chieng S, Shigeki M, SOSUI: Classification and secondary structure prediction system for membrane proteins, Bioinformatics 14:378-379, 1998.
31. Hua SJ, Sun ZR, Support vector machine approach for protein subcellular localization prediction, Bioinformatics 17:721-728, 2001.
32. Huang Y, Li YD, Prediction of protein subcellular locations using fuzzy k-NN method, Bioinformatics 20(1):21-28, 2004.
33. Lio P, Vannucci M, Wavelet change-point prediction of transmembrane proteins, Bioinformatics 16:376-382, 2000.
34. Liu H, Wang M, Chou KC, Low-frequency fourier spectrum for predicting membrane protein types. Biochem Biophys Res Commun 336:737-739, 2005.
35. Luo RY, Feng ZP, Liu JK, Prediction of protein strctural class by amino acid and polypeptide composition, Eur J Biochem 269:4219-4225, 2002.
36. Matthews BW, Comparison of predicted and observed secondary structure of T4 phage lysozyme, Biochim Biophys Acta 405:442-451, 1975.
37. Nakal K, Protein sorting signals and prediction of subcellular localization, Adv Protein Chem 54(1):277-344, 2000.
38. Nakashima H, Nishikawa K, Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies, J Mol 238:54-61, 1994.
39. Nielsen H, Brunak S, von Heijne G, Machine learning approaches for the prediction of signal peptides and other protein sorting signals, Protein Eng 12:3-9, 1997.
40. Nielsen H, Engelbrecht J, Brunak S, von Heijne G, A neural network method for identification of prokaryotic and eukaryotic signal perptides and prediction of their cleavage sites, Int J Neural Sys 8:581-599, 1997.
41. Pan YX, Zhang ZZ, Guo ZM, Feng GY, Huang ZD, He L, Application of pseudo amino acid composition for predicting protein subcellular location: Stochastic signal processing approach, J Protein Chem 22:395-402, 2003.
42. Park KJ, Kanehisa M, Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs, Bioinformatics 19(13):1656-1663, 2004.
43. Parzen E, On estimation of a probability density function and mode, Ann Math Stat 33:1065-1076, 1962.
44. Reinhardt A, Hubbard T, Using neural networks for prediction of the subcellular location of proteins, Nucleic Acids Res 26:2230-2236, 1998.
45. Rost B, Fariselli P, Casadio R, Topology prediction for helical transmembrane proteins at 86% accuracy, Protein Sci 5:1704-1718, 1996.
46. Shen HB, Chou KC, Predicting protein subnuclear location with optimized evidence-theoretic k-nearest classifier and pseudo amino acid composition, Biochem Biophys Res Commun 337:752-756, 2005.
47. Shen HB, Yang J, Liu XJ, Chou KC, Using supervised fuzzy clustering to predict protein structural classes, Biochem Biophys Res Commun 334:577-581, 2005.
48. Specht DF, Probabilistic neural network, Neural Networks 3(1):109-118, 1990.
49. Sun XD, Huang RB, Prediction of protein structural classes using support vector machines, Amino Acids DOI: 10.1007/S00726-005-0239-0, 2006.
50. Wang M, Yang J, Xu ZJ, Chou KC, SLLE for predicting membrane protein types, J Theor Biol 232:7-15, 2005.
51. Xiao, X, Shao S, Ding Y, Huang Z, Huang Y, Chou KC, Using complexity measure factor to predict protein subcellular location, Amino Acids 28:57-61, 2005.
52. Xiao X, Shao SH, Ding YS, Huang ZD, Chou KC, Using cellular automata images and pseudo amino acid composition to predict protein sub-cellular location, Amino Acids 30:49-54, 2006.
53. Xiao X, Shao SH, Huang ZD, Chou KC, Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor, J Comput Chem 27:478-482,2006.
54. Yuan Z, Prediction of protein subcellular locations using markov chain models, FEBS Letters 451:23-26, 1999.
55. Zhou GP, An intriguing controversy over protein structural class prediction, J Protein Chem 17:729-738, 1998.
56. Zhou GP, Assa-Munt N, Some insights into protein structural class prediction, PROTEINS: Struct Function Genet 44:57-59, 2001.
57. Zhou GP, Cal YD, Predicting protease types by hybridizing gene ontology and pseudo amino acid composition, PROTEINS: Struct Function Bioinform 63:681-684, 2006.
58. Zhou GP, Doctor K, Subcellular location prediction of apoptosis proteins, PROTEINS: Struct Function Genet 50:44-48, 2003.