Using Over-Represented Tetrapeptides to Predict Protein Submitochondria Locations

Acta Biotheoretica

Volumn 61, Issue 2, 2013, Pages 259-268

  Lin, Hao ^a   Chen, Wei ^b   Yuan, Lu Feng ^a   Li, Zi Qiang ^a,c   Ding, Hui ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b HEBEI UNITED UNIVERSITY   (China)

^c SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Binomial distribution; Submitochondria location; Support vector machine; Tetrapeptide

Indexed keywords

OLIGOPEPTIDE;

BIOINFORMATICS; DATA SET; EUKARYOTE; MITOCHONDRION; NUMERICAL MODEL; PROTEIN;

ARTICLE; METABOLISM; SUBMITOCHONDRIAL PARTICLE; SUPPORT VECTOR MACHINE; THEORETICAL MODEL;

MODELS, THEORETICAL; OLIGOPEPTIDES; SUBMITOCHONDRIAL PARTICLES; SUPPORT VECTOR MACHINES;

EUKARYOTA;

EID: 84878789801     PISSN: 00015342     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10441-013-9181-9     Document Type: Article

References (34)

1. Chou KC, Shen HB (2007) Recent progress in protein subcellular location prediction. Anal Biochem 370: 1-16.
2. Chou KC, Shen HB (2008) Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc 3: 153-162.
3. Chou KC, Zhang CT (1995) Review: prediction of protein structural classes. Crit Rev Biochem Mol Biol 30: 275-349.
4. Ding H, Liu L, Guo FB, Huang J, Lin H (2011) Identify Golgi protein types with modified Mahalanobis discriminant algorithm and pseudo amino acid composition. Protein Pept Lett 18: 58-63.
5. Du P, Li Y (2006) Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioinform 7: 518.
6. Du P, Cao S, Li Y (2009) SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm. J Theor Biol 261: 330-335.
7. Du P, Li T, Wang X (2011) Recent progress in predicting protein sub-subcellular locations. Expert Rev Proteomics 8: 391-404.
8. Fan GL, Li QZ (2012) Predicting protein submitochondria locations by combining different descriptors into the general form of Chou's pseudo amino acid composition. Amino Acids 43: 545-555.
9. Fan RE, Chen PH, Lin CJ (2005) Working set selection using the second order information for training SVM. J Mach Learn Res 6: 1889-1918.
10. Feng Y, Luo L (2008) Use of tetrapeptide signals for protein secondary-structure prediction. Amino Acids 35: 607-614.
11. Henze K, Martin W (2003) Evolutionary biology: essence of mitochondria. Nature 426: 127-128.
12. Huang WL, Tung CW, Huang HL, Hwang SF, Ho SY (2007) ProLoc: prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features. Biosystems 90: 573-581.
13. Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinform 9: 80.
14. Huang WL, Tung CW, Huang HL, Ho SY (2009) Predicting protein subnuclear localization using GO-amino-acid composition features. Biosystems 98: 73-79.
15. Jiang X, Wei R, Zhao Y, Zhang T (2008) Using Chou's pseudo amino acid composition based on approximate entropy and an ensemble of AdaBoost classifiers to predict protein subnuclear location. Amino Acids 34: 669-675.
16. Lei Z, Dai Y (2005) An SVM-based system for predicting protein subnuclear localizations. BMC Bioinform 6: 291.
17. Lei Z, Dai Y (2006) Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinform 7: 491.
18. Li FM, Li QZ (2008) Using pseudo amino acid composition to predict protein subnuclear location with improved hybrid approach. Amino Acids 34: 119-125.
19. Mei S (2012) Multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization. J Theor Biol 293: 121-130.
20. Mei S, Fei W (2010) Amino acid classification based spectrum kernel fusion for protein subnuclear localization. BMC Bioinform Suppl 1: S17.
21. Nanni L, Lumini A (2008) Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization. Amino Acids 34: 653-660.
22. Polianskyte Z, Peitsaro N, Dapkunas A, Liobikas J, Soliymani R, Lalowski M, Speer O, Seitsonen J, Butcher S, Cereghetti GM, Linder MD, Merckel M, Thompson J, Eriksson O (2009) LACTB is a filament-forming protein localized in mitochondria. Proc Natl Acad Sci USA 106: 18960-18965.
23. Rackovsky S (1993) On the nature of protein folding code. Proc Natl Acad Sci USA 90: 644-648.
24. Shen HB, Chou KC (2005) Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition. Biochem Biophys Res Commun 337: 752-756.
25. Shen HB, Chou KC (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.
26. Shi Y (2002) A conserved tetrapeptide motif: potentiating apoptosis through IAP-binding. Cell Death Differ 9: 93-95.
27. Shi SP, Qiu JD, Sun XY, Huang JH, Huang SY, Suo SB, Liang RP, Zhang L (2011) Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction. Biochim Biophys Acta 1813: 424-430.
28. Stuart GW, Moffett K, Leader JJ (2002) A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol Biol Evol 19: 554-562.
29. UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75.
30. van Dijk AD, Bosch D, ter Braak CJ, van der Krol AR, van Ham RC (2008) Predicting sub-Golgi localization of type II membrane proteins. Bioinformatics 24: 1779-1786.
31. Verhagen AM, Kratina TK, Hawkins CJ, Silke J, Ekert PG, Vaux DL (2007) Identification of mammalian mitochondrial proteins that interact with IAPs via N-terminal IAP binding motifs. Cell Death Differ 14: 348-357.
32. Wang G, Dunbrack RL Jr (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 33: W94-W98.
33. Zakeri P, Moshiri B, Sadeghi M (2011) Prediction of protein submitochondria locations based on data fusion of various features of sequences. J Theor Biol 269: 208-216.
34. Zeng YH, Guo YZ, Xiao RQ, Yang L, Yu LZ, Li ML (2009) Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J Theor Biol 259: 366-372.