PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3613-3617

  Gardy, Jennifer L ^a   Spencer, Cory ^a   Wang, Ke ^a   Ester, Martin ^a   Tusnády, Gábor E ^b   Simon, István ^b   Hua, Sujun ^c   deFays, Katalin ^d   Lambert, Christophe ^d   Nakai, Kenta ^e   Brinkman, Fiona S L ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b INSTITUTE OF ENZYMOLOGY   (Hungary)

^c YALE UNIVERSITY   (United States)

^d UNIVERSITY OF NAMUR   (Belgium)

^e UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; MEMBRANE PROTEIN; SIGNAL PEPTIDE;

ACCURACY; ALPHA HELIX; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; AUTOMATION; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DRUG RESEARCH; EQUIPMENT DESIGN; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; INTERNET; LICENCE; MATHEMATICAL COMPUTING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MOTIF; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; CHEMISTRY; EVALUATION; METHODOLOGY; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; REPRODUCIBILITY; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

BACTERIAL PROTEINS; DATABASES, PROTEIN; GRAM-NEGATIVE BACTERIA; INTERNET; MEMBRANE PROTEINS; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 0042622254     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg602     Document Type: Article

References (18)

1. Nakai,K. (2000) Protein sorting signals and prediction of subcellular localization. Adv. Protein. Chem., 54, 277-344.
2. Eisenhaber,F. and Bork,P. (1998) Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol., 8, 69-70.
3. Nakai,K. and Kanehisa,M. (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins, 11, 95-110.
4. Horton,P. and Nakai,K. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci., 24, 34-36.
5. Bannai,H., Tamada,Y., Maruyama,O., Nakai,K. and Miyano,S. (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics, 18, 298-305.
6. Emanuelsson,O., Nielsen,H., Brunak,S. and von Heijne,G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300, 1005-1016.
7. Reinhardt,A. and Hubbard,T. (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res., 26, 2230-2236.
8. Hua,S. and Sun,Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics, 17, 721-728.
9. Emanuelsson,O. (2002) Predicting protein subcellular localisation from amino acid sequence information. Brief. Bioinform., 3, 361-376.
10. Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural Syst., 8, 581-599.
11. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
12. Nair,R. and Rost,B. (2002) Sequence conserved for subcellular localization. Protein Sci., 11, 2836-2847.
13. Hofmann,K., Bucher,P., Falquet,L. and Bairoch,A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res., 27, 215-219.
14. von Heijne,G. (1994) Signals for protein targeting into and across membranes. Subcell. Biochem., 22, 1-19.
15. Tusnady,G.E. and Simon,I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 283, 489-506.
16. Tusnady,G.E. and Simon,I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
17. Bernstein,H.D. (1998) Membrane protein biogenesis: the exception explains the rules. Proc. Natl Acad. Sci. USA, 95, 14587-14589.
18. Menne,K.M.L., Hermjakob,H. and Apweiler,R. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics, 16, 741-742.