DOI: 10.1002/jcb.10790. Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo‐amino acid composition

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

10.1002/jcb.10790

Crossref journal-article

Wiley

Journal of Cellular Biochemistry (311)

Abstract

AbstractRecent advances in large‐scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Since the functions of these proteins are closely correlated with their subcellular localizations, many efforts have been made to develop a variety of methods for predicting protein subcellular location. In this study, based on the strategy by hybridizing the functional domain composition and the pseudo‐amino acid composition (Cai and Chou [2003]: Biochem. Biophys. Res. Commun. 305:407–411), the Intimate Sorting Algorithm (ISort predictor) was developed for predicting the protein subcellular location. As a showcase, the same plant and non‐plant protein datasets as investigated by the previous investigators were used for demonstration. The overall success rate by the jackknife test for the plant protein dataset was 85.4%, and that for the non‐plant protein dataset 91.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross validation test procedure, further confirming that such a hybrid approach may become a very useful high‐throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. © 2004 Wiley‐Liss, Inc.

Bibliography

Chou, K., & Cai, Y. (2004). Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudoâamino acid composition. Journal of Cellular Biochemistry, 91(6), 1197â1203. Portico.

Authors 2

Kuo‐Chen Chou (first)
Yu‐Dong Cai (additional)

References 30 Referenced 66

{'key': 'e_1_2_7_2_1', 'volume-title': '“Molecular Biology of the Cell, chap. 1.”', 'author': 'Alberts B', 'year': '1994'} / “Molecular Biology of the Cell, chap. 1.” by Alberts B (1994)
10.1093/nar/29.1.37
10.1016/0006-291X(76)90001-2
10.1016/S0006-291X(03)00775-7
10.1006/jmbi.1996.0804
10.1016/S0092-8674(00)80572-3
10.1016/S0092-8674(00)81417-8
10.1006/jtbi.1993.1053
10.1002/prot.340210406
10.1002/prot.1035
{'key': 'e_1_2_7_12_1', 'first-page': '57', 'volume-title': 'Gene cloning & expression technologies', 'author': 'Chou KC', 'year': '2002'} / Gene cloning & expression technologies by Chou KC (2002)
10.1074/jbc.M204161200
10.1002/prot.10500
10.1093/protein/12.2.107
10.1021/pr0255710
10.3109/10409239509083488
10.1016/S0959-440X(97)80057-7
10.1006/jmbi.2000.3903
{'key': 'e_1_2_7_20_1', 'volume-title': 'Molecular cell biology, chap. 3', 'author': 'Lodish H', 'year': '1995'} / Molecular cell biology, chap. 3 by Lodish H (1995)
{'key': 'e_1_2_7_21_1', 'first-page': '322', 'volume-title': 'Multivariate analysis', 'author': 'Mardia KV', 'year': '1979'} / Multivariate analysis by Mardia KV (1979)
10.1093/nar/29.1.58
10.1016/S0968-0004(98)01336-X
10.1016/S0888-7543(05)80111-9
10.1006/jmbi.1994.1267
10.1023/A:1025350409648
10.1093/nar/26.9.2230
{'key': 'e_1_2_7_28_1', 'volume-title': 'Molecular biology of the gene', 'author': 'Watson JD', 'year': '1987'} / Molecular biology of the gene by Watson JD (1987)
10.1023/A:1020713915365
10.1002/prot.1071
10.1002/prot.10251

Dates

Type	When
Created	21 years, 5 months ago (March 24, 2004, 3:02 a.m.)
Deposited	1 year, 10 months ago (Oct. 9, 2023, 10:59 a.m.)
Indexed	1 year, 2 months ago (May 28, 2024, 10:28 a.m.)
Issued	21 years, 5 months ago (March 4, 2004)
Published	21 years, 5 months ago (March 4, 2004)
Published Online	21 years, 5 months ago (March 4, 2004)
Published Print	21 years, 4 months ago (April 15, 2004)

Funders 0

None

BibTeX

@article{Chou_2004, title={Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo‐amino acid composition}, volume={91}, ISSN={1097-4644}, url={http://dx.doi.org/10.1002/jcb.10790}, DOI={10.1002/jcb.10790}, number={6}, journal={Journal of Cellular Biochemistry}, publisher={Wiley}, author={Chou, Kuo‐Chen and Cai, Yu‐Dong}, year={2004}, month=mar, pages={1197–1203} }

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