Prediction and Classification of Protein Subcellular Location - Sequence-Order Effect and Pseudo Amino Acid Composition

Journal of Cellular Biochemistry

Volumn 90, Issue 6, 2003, Pages 1250-1260

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

^a GORDON LIFE SCIENCE INSTITUTE   (United States)

^b Tianjin Inst Bioinfo Drug Discov   (China)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Augmented covariant discriminant algorithm; Bioinformatics; High throughput tool; Organelles; Proteomics; Subcellular compartments

Indexed keywords

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOINFORMATICS; CELL MEMBRANE; CELL NUCLEUS; CELL VACUOLE; CELL WALL; CELLULAR DISTRIBUTION; CENTRIOLE; CHLOROPLAST; COMPARATIVE STUDY; CYTOPLASM; CYTOSKELETON; ENDOPLASMIC RETICULUM; EXTRACELLULAR MATRIX; GOLGI COMPLEX; LYSOSOME; MITOCHONDRION; PEROXISOME; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; CELL COMPARTMENTATION; CELL PHYSIOLOGY; DATABASES, FACTUAL; HUMANS; MODELS, BIOLOGICAL; PROTEINS; SUBCELLULAR FRACTIONS;

EID: 0345305854     PISSN: 07302312     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcb.10719     Document Type: Article

References (44)

1. Bahar I, Atilgan AR, Jernigan RL, Erman B. 1997. Understanding the recognition of protein structural classes by amino acid composition. Proteins: Structure, Function, and Genetics 29:172-185.
2. Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res 25:31-36.
3. Cai YD. 2001. Is it a paradox or misinterpretation. Proteins: Structure, Function, and Genetics 43:336-338.
4. Cai YD, Liu XJ, Xu XB, Chou KC. 2002. Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. J Cell Biochem 84:343-348.
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 PY. 1989. Prediction of protein structural classes from amino acid composition. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press. pp 549-586.
7. Chou KC. 1995. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Structure, Function, and Genetics 21:319-344.
8. Chou KC. 1999a. A key driving force in determination of protein structural classes. Biochem Biophysical Res Commun 264:216-224.
9. Chou KC. 1999b. Using pair-coupled amino acid composition to predict protein secondary structure content. J Protein Chem 18:473-480.
10. Chou KC. 2000a. Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochemical Biophysical Res Commun 278:477-483.
11. Chou KC. 2000b. Review: Prediction of protein structural classes and subcellular locations. Curr Protein Peptide Sci 1:171-208.
12. Chou KC. 2001. Prediction of protein cellular attributes using pseudo-amino-acid-composition. Proteins: Structure, Function, and Genetics 43:246-255 (Erratum: Proteins: Struct Funct Genet 2001, Vol. 44:60).
13. Chou KC. 2001. Prediction of protein cellular attributes using pseudo-amino-acid-composition. Proteins: Structure, Function, and Genetics 43:246-255 (Erratum: Proteins: Struct Funct Genet 2001, Vol. 44:60).
14. Chou KC. 2002a. A new branch of proteomics: prediction of protein cellular attributes. Chapter 4. In: Weinrer PW, Lu Q, editors. Gene cloning and expression technologies. Westborough, MA: Eaton Publishing. pp 57-70.
15. Chou KC. 2002b. Prediction of protein signal sequences. Curr Protein Peptide Sci 3:615-622.
16. 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.
17. Chou KC, Cai YD. 2003. Predicting protein quaternary structure by pseudo amino acid composition. Proteins: Structure, Function, and Genetics 53:282-289.
18. Chou KC, Elrod DW. 1999a. Prediction of membrane protein types and subcellular locations. Proteins: Structure, Function, and Genetics 34:137-153.
19. Chou KC, Elrod DW. 1999b. Protein subcellular location prediction. Protein Eng 12:107-118.
20. Chou KC, Elrod DW. 2002. Bioinformatical analysis of G-protein-coupled receptors. J Proteome Res 1:429-433.
21. Chou KC, Elrod DW. 2003. Prediction of enzyme family classes. J Proteome Res 2:183-190.
22. Chou KC, Zhang CT. 1994. Predicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem 269:22014-22020.
23. Chou KC, Zhang CT. 1995. Review: Prediction of protein structural classes. Crit Rev Biochem Mol Biol 30:275-349.
24. Chou KC, Liu W, Maggiora GM, Zhang CT. 1998. Prediction and classification of domain structural classes. Proteins: Structure, Function, and Genetics 31:97-103.
25. Claros MG, Brunak S, von Heijne G. 1997. Prediction of N-terminal protein sorting signals. Curr Opin Struct Biol 7:394-398.
26. Elrod DW, Chou KC. 2002. A study on the correlation of G-protein-coupled receptor types with amino acid composition. Protein Eng 15:713-715.
27. Krigbaum WR, Knutton SP. 1973. Prediction of the amount of secondary structure in a globular protein from its amino acid composition. Proc Natl Acad Sci USA 70:2809-2813.
28. Liu W, Chou KC. 1998. Prediction of protein structural classes by modified Mahalanobis discriminant algorithm. J Protein Chem 17:209-217.
29. Liu W, Chou KC. 1999. Protein secondary structural content prediction. Protein Eng 12:1041-1050.
30. Mardia KV, Kent JT, Bibby JM. 1979. Multivariate analysis. London, UK: Academic Press. pp 322, 381.
31. 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 Res 29:58-60.
32. Muskal SM, Kim S-H. 1992. Predicting protein secondary structure content: A tandem neural network approach. J Mol Biol 225:713-727.
33. Nakai K, Kanehisa M. 1992. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14:897-911.
34. 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.
35. Nakashima H, Nishikawa K, Ooi T. 1986. The folding type of a protein is relevant to the amino acid composition. J Biochem 99:152-162.
36. 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.
37. Radford T. 2003. Metaphors and dreams. The Scientist 17:24-26.
38. Reinhardt A, Hubbard T. 1998. Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res 26:2230-2236.
39. Tanford C. 1962. Contribution of hydrophobic interaction to the stability of the globular conformation of proteins. J Amer Chem Soc 84:4240-4274.
40. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
41. Zhang CT, Zhang Z, He Z. 1996. Prediction of the secondary structure content of globular proteins based on structural classes. J Protein Chem 15:775-786.
42. Zhou GP. 1998. An intriguing controversy over protein structural class prediction. J Protein Chem 17:729-738.
43. Zhou GP, Assa-Munt N. 2001. Some insights into protein structural class prediction. Proteins: Structure, Function, and Genetics 44:57-59.
44. Zhou GP, Doctor K. 2003. Subcellular location prediction of apoptosis proteins. Proteins: Structure, Function, and Genetics 50:44-48.