Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition

Journal of Cellular Biochemistry

Volumn 91, Issue 6, 2004, Pages 1197-1203

  Chou, Kuo Chen ^a,b   Cai, Yu Dong ^c,d  

^a GORDON LIFE SCIENCE INSTITUTE   (United States)

^b Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD)   (China)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Functional domain composition; InterPro database; Intimate Sorting Algorithm; Protein subcellular location; Pseudo amino acid composition

Indexed keywords

VEGETABLE PROTEIN; PROTEIN;

AMINO ACID COMPOSITION; ARTICLE; BIOINFORMATICS; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEOMICS; ALGORITHM; BIOLOGY; CELL STRUCTURE; CHEMICAL MODEL; CHEMISTRY; GENOME; METABOLISM; METHODOLOGY; PREDICTION AND FORECASTING; PROBABILITY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

ALGORITHMS; CELLULAR STRUCTURES; COMPUTATIONAL BIOLOGY; GENOME; MARKOV CHAINS; MODELS, CHEMICAL; PREDICTIVE VALUE OF TESTS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 7444264582     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.10790     Document Type: Article

References (30)

1. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD. 1994. Molecular biology of the cell, chap. 1. New York & London: Garland Publishing.
2. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MDR, Durbin R, Falquet L, Fleischmann W, Gouzy L, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJA, Zdobnov EM. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29:37-40.
3. Blobel G. 1976. Extraction from free ribosomes of a factor mediating ribosome detachment from rough microsomes. Biochem Biophys Res Comm 68:1-7.
4. Cai YD, Chou KC. 2003. Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem Biophys Res Comm 305: 407-411.
5. Cedano J, Aloy P, P'erez-Pons JA, Querol E. 1997. Relation between amino acid composition and cellular location of proteins. J Mol Biol 266:594-600.
6. Chou JJ, Li H, Salvesen GS, Yuan J, Wagner G. 1999. Solution structure of BID, an intracellular amplifier of apoptotic signaling. Cell 96:615-624.
7. Chou JJ, Matsuo H, Duan H, Wagner G. 1998. Solution structure of the RAIDD CARD and model for CARD/ CARD interaction in caspase-2 and caspase-9 recruitment. Cell 94:171-180.
8. Chou JJ, Zhang CT. 1993. A joint prediction of the folding types of 1,490 human proteins from their genetic codons. J Theor Biol 161:251-262.
9. Chou KC. 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.
10. Chou KC. 2001. Prediction of protein cellular attributes using pseudo-amino-acid-composition, (Erratum Vol. 44, 60). Proteins: Struct Funct Genet 43:246-255.
11. Chou KC. 2002. A new branch of proteomics: Prediction of protein cellular attributes. In: Weinrer PW, Lu Q, editors. Gene cloning & expression technologies. Westborough, MA: Eaton Publishing, pp 57-70.
12. Chou KC, Cai YD. 2002. Using functional domain composition and support vector machines for prediction of protein subcellular location. J Biol Chem 277:45765-45769.
13. Chou KC, Cai YD. 2003. Predicting protein quaternary structure by pseudo amino acid composition. Proteins 53:282-289.
14. Chou KC, Elrod DW. 1999. Protein subcellular location prediction. Protein Engineering 12:107-118.
15. Chou KC, Elrod DW. 2003. Prediction of enzyme family classes. J Proteome Res 2:183-190.
16. Chou KC, Zhang CT. 1995. Review: Prediction of protein structural classes. Crit Rev Biochem Mol Biol 30:275-349.
17. Claros MG, Brunak S, von Heijne G. 1997. Prediction of N-terminal protein sorting signals. Curr Opin Struct Biol 7:394-398.
18. Emanuellson O, Nielsen H, Brunak S, von Heijne G. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
19. Lodish H, Baltimore D, Berk A, Zipursky SL, Matsudaira P, Darnell J. 1995. Molecular cell biology, chap. 3. New York: Scientific American Books.
20. Mardia KV, Kent JT, Bibby JM. 1979. Multivariate analysis. London: Academic Press, pp 322-381.
21. Murvai J, Vlahovicek K, Barta E, Pongor S. 2001. The SBASE protein domain library, release 8.0: A collection of annotated protein sequence segments. Nucleic Acids Research 29:58-60.
22. Nakai K, Horton P. 1999. PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24:34-36.
23. Nakai K, Kanehisa M. 1992. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14:897-911.
24. Nakashima H, Nishikawa K. 1994. Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J Mol Biol 238:54-61.
25. Pan YX, Zhang ZZ, Guo ZM, Feng GY, Huang ZD, He L. 2003. Application of pseudo amino acid composition for predicting protein subcellular location: Stochastic signal processing approach. J Protein Chem 22:395-402.
26. Reinhardt A, Hubbard T. 1998. Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res 26:2230-2236.
27. Watson JD, Hopkins NH, Roberts JW, Steitz JA, Weiner AM. 1987. Molecular biology of the gene 4th edn. Menlo Park, CA: Benjamin/Cummings Publishing Company, Inc.
28. Zhou GP. 1998. An intriguing controversy over protein structural class prediction. J Protein Chem 17:729-738.
29. Zhou GP, Assa-Munt N. 2001. Some insights into protein structural class prediction. Proteins: Struct Funct Genet 44:57-59.
30. Zhou GP, Doctor K. 2003. Subcellular location prediction of apoptosis proteins. Proteins: Struct Funct Genet 50: 44-48.