References:
- Hideo Bannai, Yoshinori Tamada, Osama Maruyama, Kenta Nakai, and Satoru Miyano (2002)
Extensive feature detection of N-terminal protein sorting signals
Bioinformatics 18: 298-305
Protein localization (iPSORT)
- Jannick Dyrløv Bendtsen, Lars Juhl Jensen, Nikolaj Blom, Gunnar von Heijne, and Søren Brunak (2004)
Feature based prediction of non-classical and leaderless protein secretion
Protein Eng. Des. Sel. 17: 349-356
Mammalian secretory protein (SecretomeP)
- Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne, and Søren Brunak (2004)
Improved prediction of signal peptides: SignalP 3.0
J. Mol. Biol. 340: 783-795
Signal peptide (SignalP 3.0)
- Manoj Bhasin and G.P.S. Raghava (2004)
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
Nucl. Acids Res. 32: W414-W419
Protein localization (ESLpred)
- Rita Casadio, Piero Fariselli, Giacomo Finocchiaro, and Pier Luigi Martelli (2003)
Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria
Protein Sci. 12(6): 1158-1168
Protein localization (Hunter)
- J. Cedano, P. Aloy, J.A. Perez-Pons, and E. Querol (1997)
Relation between amino acid composition and cellular location of proteins
J. Mol. Biol. 266: 594-600
Protein localization (ProtLock)
- Kuo-Chen Chou and Yu-Dong Cai (2004)
Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition
J. Cell. Biochem. 91: 1197-1203
Protein localization (ISort)
- K.C. Chou and D.W. Elrod (1998)
Using discriminant function for prediction of subcellular location of prokaryotic proteins
Biochem. Biophys. Res. Commun. 252: 63-68
Protein localization
- M.G. Claros and P. Vincens (1996)
Computational method to predict mitochondrially imported proteins and their targeting sequences
Eur. J. Biochem. 241: 779-786
Organelle targeting signal
- Murat Cokol, Rajesh Nair and Burkhard Rost (2000)
Finding nuclear localization signals
EMBO Rep. 1: 411-415
Nuclear targeting signal (PredictNLS)
- Olof Emanuelsson, Henrik Nielsen and Gunnar von Heijne (1999)
ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
Protein Sci. 8: 978-984
Organelle targeting signal (ChloroP)
- Olof Emanuelsson, Henrik Nielsen, Søren Brunak and Gunnar von Heijne (2000)
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
J. Mol. Biol. 300: 1005-1016
Protein localization (TargetP)
- Olof Emanuelsson and Gunnar von Heijne (2001)
Prediction of organellar targeting signals
Biochim. Biophys. Acta 1541: 114-119
Organelle targeting signal
- Z.P. Feng and C.T. Zhang (2001)
Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids
Int. J. Biol. Macromol. 28: 255-261
Protein localization
- Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gábor E. Tusnady, István Simon, Sujun Hua, Katalin deFays, Christophe Lambert, Kenta Nakai, and Fiona S.L. Brinkman (2003)
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria
Nucl. Acids Res. 31: 3613-3617
Protein localization (PSORT-B)
- Takatsugu Hirokawa, Seah Boon-Chieng, and Shigeki Mitaku (1998)
SOSUI: classification and secondary structure prediction system for membrane proteins
Bioinformatics 14: 378-379
Signal peptide (SOSUI)
- Paul Horton and Kenta Nakai (1996)
A probabilistic classification system for predicting the cellular localization sites of proteins
Proc. Int. Conf. Intell. Syst. Mol. Biol. 4: 109-115
Protein localization (PSORT II)
- Paul Horton and Kenta Nakai (1997)
Better prediction of protein cellular localization sites with the k nearest neighbors classifier
Proc. Int. Conf. Intell. Syst. Mol. Biol. 5: 147-152
Protein localization (PSORT II)
- Sujun Hua and Zhirong Sun (2001)
Support vector machine approach for protein subcellular localization prediction
Bioinformatics 17: 721-728
Protein localization (SubLoc)
- B. Jagla and J. Schuchhardt (2000)
Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
Bioinformatics 16: 245-250
Signal peptide (ACNpredictor)
- D.A. Jans, C.Y. Xiao and M.H. Lam (2000)
Nuclear targeting signal recognition: a key control point in nuclear transport?
Bioessays 22: 532-544
Nuclear targeting signal
- Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner (2004)
Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers
Bioinformatics 20: 547-556
Protein localization (Proteome Analyst)
- Rajesh Nair and Burkhard Rost (2004)
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets
Nucl. Acids Res. 32: W517-W521
Protein localization (LOCnet and LOCtarget)
- Kenta Nakai and Paul Horton (1999)
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization
Trends Biochem. Sci. 24: 34-36
Protein localization (PSORT II)
- Kenta Nakai and Minoru Kanehisa (1991)
Expert system for predicting protein localization sites in Gram-negative bacteria
Prot. Struct. Funct. Genet. 11: 95-110
Protein localization (PSORT)
- Kenta Nakai and Minoru Kanehisa (1992)
A knowledge base for predicting protein localization sites in eukaryotic cells
Genomics 14: 897-911
Protein localization (PSORT)
- Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, and Gunnar von Heijne (1997)
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Protein Eng. 10: 1-6
Signal peptide (SignalP 1.1)
- Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, and Gunnar von Heijne (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
Signal peptide (SignalP 1.1)
- Henrik Nielsen, Søren Brunak, and Gunnar von Heijne (1999)
Machine learning approaches to the prediction of signal peptides and other protein sorting signals
Protein Eng. 12: 3-9
Signal peptide (SignalP 2.0)
- D. Perlman and H.O. Halvorson (1983)
A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides
J. Mol. Biol. 167: 391-409
Signal peptide ("-3,-1 rule")
- A. Reinhardt and T. Hubbard (1998)
Using neural networks for prediction of the subcellular location of proteins
Nucl. Acid. Res. 26: 2230-2236
Protein localization (NNPSL)
- Gisbert
Schneider, Sara Sjöling, Erik Wallin, Paul Wrede, Elzbieta Glaser, and Gunnar von Heijne (1998)
Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides
Proteins 30: 49-60
Organelle targeting signal
- Gunnar von Heijne (1983)
Patterns of amino acids near signal-sequence cleavage sites
Eur. J. Biochem. 133: 17-21
Signal peptide ("-3,-1 rule")
- William C. Wimley (2002)
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures
Protein Sci. 11: 301-312
Protein localization
- Chin-Sheng Yu, Chih-Jen Lin, and Jenn-Kang Hwang (2004)
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions
Protein Sci. 13: 1402-1406
Protein localization (CELLO)
- Yufeng Zhai and Milton H. Saier, Jr. (2002)
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
Protein Sci. 11: 2196-2207
Protein localization (BBF)
Latest update of content: September 20, 2005
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