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

被引:75
作者
Chou, KC
Cai, YD
机构
[1] Gordon Life Sci Inst, San Diego, CA 92130 USA
[2] TIBDD, Tianjin, Peoples R China
[3] Chinese Acad Sci, Shanghai Res Ctr Biotechnol, Shanghai 200233, Peoples R China
[4] UMIST, Biomol Sci Dept, Manchester M60 1QD, Lancs, England
关键词
intimate sorting algorithm; protein subcellular location; functional domain composition; pseudo-amino acid composition; InterPro database;
D O I
10.1002/jcb.10790
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Recent 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 clatasetsas 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. J. Cell. Biochem. 91: 1197-1203, 2004. (C) 2004 Wiley-Liss, Inc.
引用
收藏
页码:1197 / 1203
页数:7
相关论文
共 30 条
[1]  
ALBERTS B, 1994, MOL BIOL CELL, pCH1
[2]  
[Anonymous], 1987, Molecular Biology of the Gene
[3]   The InterPro database, an integrated documentation resource for protein families, domains and functional sites [J].
Apweiler, R ;
Attwood, TK ;
Bairoch, A ;
Bateman, A ;
Birney, E ;
Biswas, M ;
Bucher, P ;
Cerutti, T ;
Corpet, F ;
Croning, MDR ;
Durbin, R ;
Falquet, L ;
Fleischmann, W ;
Gouzy, J ;
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 .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :37-40
[4]   EXTRACTION FROM FREE RIBOSOMES OF A FACTOR MEDIATING RIBOSOME DETACHMENT FROM ROUGH MICROSOMES [J].
BLOBEL, G .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 1976, 68 (01) :1-7
[5]   Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition [J].
Cai, YD ;
Chou, KC .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 305 (02) :407-411
[6]   Relation between amino acid composition and cellular location of proteins [J].
Cedano, J ;
Aloy, P ;
PerezPons, JA ;
Querol, E .
JOURNAL OF MOLECULAR BIOLOGY, 1997, 266 (03) :594-600
[7]   Solution structure of BID, an intracellular amplifier of apoptotic signaling [J].
Chou, JJ ;
Li, HL ;
Salvesen, GS ;
Yuan, JY ;
Wagner, G .
CELL, 1999, 96 (05) :615-624
[8]   Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment [J].
Chou, JJ ;
Matsuo, H ;
Duan, H ;
Wagner, G .
CELL, 1998, 94 (02) :171-180
[9]   A JOINT PREDICTION OF THE FOLDING TYPES OF 1490 HUMAN PROTEINS FROM THEIR GENETIC CODONS [J].
CHOU, JJW ;
ZHANG, CT .
JOURNAL OF THEORETICAL BIOLOGY, 1993, 161 (02) :251-262
[10]   Predicting protein quaternary structure by pseudo amino acid composition [J].
Chou, KC ;
Cai, YD .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2003, 53 (02) :282-289