Protein subcellular localization prediction based on compartment-specific features and structure conservation

[1]  Kuo-Chen Chou,et al.  Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.

[2]  K. Chou,et al.  Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. , 2007, Biochemical and biophysical research communications.

[3]  K. Chou,et al.  Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. , 2007, Journal of proteome research.

[4]  Wen-Lian Hsu,et al.  NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition , 2006, BMC Bioinformatics.

[5]  J. Gardy,et al.  Methods for predicting bacterial protein subcellular localization , 2006, Nature Reviews Microbiology.

[6]  Doheon Lee,et al.  PLPD: reliable protein localization prediction from imbalanced and overlapped datasets , 2006, Nucleic acids research.

[7]  Jenn-Kang Hwang,et al.  Prediction of protein subcellular localization , 2006, Proteins.

[8]  Piero Fariselli,et al.  BaCelLo: a balanced subcellular localization predictor , 2006, ISMB.

[9]  Kuo-Chen Chou,et al.  Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. , 2006, Journal of proteome research.

[10]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[11]  Pierre Baldi,et al.  DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks , 2006, Data Mining and Knowledge Discovery.

[12]  Randy Schekman,et al.  Protein Translocation Across Biological Membranes , 2005, Science.

[13]  Michael T. Hallett,et al.  Refining Protein Subcellular Localization , 2005, PLoS Comput. Biol..

[14]  Søren Brunak,et al.  Non-classical protein secretion in bacteria , 2005, BMC Microbiology.

[15]  Wen-Lian Hsu,et al.  HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence , 2005, Bioinform..

[16]  S. Brunak,et al.  Prediction of twin-arginine signal peptides , 2005, BMC Bioinformatics.

[17]  David R. Westhead,et al.  TMB-Hunt: a web server to screen sequence sets for transmembrane β-barrel proteins , 2005, Nucleic Acids Res..

[18]  Gajendra P. S. Raghava,et al.  PSLpred: prediction of subcellular localization of bacterial proteins , 2005, Bioinform..

[19]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[20]  B. Rost,et al.  Mimicking cellular sorting improves prediction of subcellular localization. , 2005, Journal of molecular biology.

[21]  Kuo-Chen Chou,et al.  Predicting protein localization in budding Yeast , 2005, Bioinform..

[22]  Martin Ester,et al.  Sequence analysis PSORTb v . 2 . 0 : Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis , 2004 .

[23]  Silvio C. E. Tosatto,et al.  The SSEA server for protein secondary structure alignment , 2005, Bioinform..

[24]  Lutz Schmitt,et al.  Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (Review) , 2005, Molecular membrane biology.

[25]  Christophe G. Lambert,et al.  PSORTdb: a protein subcellular localization database for bacteria , 2004, Nucleic Acids Res..

[26]  Zemin Zhang,et al.  Signal peptide prediction based on analysis of experimentally verified cleavage sites , 2004, Protein science : a publication of the Protein Society.

[27]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[28]  G. Schneider,et al.  Advances in the prediction of protein targeting signals , 2004, Proteomics.

[29]  Jenn-Kang Hwang,et al.  Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions , 2004, Protein science : a publication of the Protein Society.

[30]  Zhiyong Lu,et al.  Predicting subcellular localization of proteins using machine-learned classifiers , 2004, Bioinform..

[31]  Chih-Jen Lin,et al.  Probability Estimates for Multi-class Classification by Pairwise Coupling , 2003, J. Mach. Learn. Res..

[32]  B. Rost,et al.  Better prediction of sub‐cellular localization by combining evolutionary and structural information , 2003, Proteins.

[33]  Minoru Kanehisa,et al.  Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs , 2003, Bioinform..

[34]  Bill C White,et al.  Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases , 2003, BMC Bioinformatics.

[35]  Ke Wang,et al.  PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria , 2003, Nucleic Acids Res..

[36]  Burkhard Rost,et al.  LOC3D: annotate sub-cellular localization for protein structures , 2003, Nucleic Acids Res..

[37]  W. Nickel.  The mystery of nonclassical protein secretion. A current view on cargo proteins and potential export routes. , 2003, European journal of biochemistry.

[38]  Burkhard Rost,et al.  Sequence conserved for subcellular localization , 2002, Protein science : a publication of the Protein Society.

[39]  Peer Bork,et al.  Predicting protein cellular localization using a domain projection method. , 2002, Genome research.

[40]  Satoru Miyano,et al.  Extensive feature detection of N-terminal protein sorting signals , 2002, Bioinform..

[41]  Zhirong Sun,et al.  Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..

[42]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[43]  D. Eisenberg,et al.  Localizing proteins in the cell from their phylogenetic profiles. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[44]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[45]  G. Schulz,et al.  Structure of the outer membrane protein A transmembrane domain , 1998, Nature Structural Biology.

[46]  B. Rost,et al.  Adaptation of protein surfaces to subcellular location. , 1998, Journal of molecular biology.

[47]  B. Berks.  A common export pathway for proteins binding complex redox cofactors? , 1996, Molecular microbiology.

[48]  I. Muchnik,et al.  Prediction of protein folding class using global description of amino acid sequence. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[49]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[50]  A. Pugsley.  The complete general secretory pathway in gram-negative bacteria. , 1993, Microbiological reviews.

[51]  M. Kanehisa,et al.  Expert system for predicting protein localization sites in gram‐negative bacteria , 1991, Proteins.

[52]  Eugene W. Myers,et al.  Optimal alignments in linear space , 1988, Comput. Appl. Biosci..

[53]  B. Matthews.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.

[54]  Wen-Lian Hsu,et al.  PROTEIN SUBCELLULAR LOCALIZATION PREDICTION BASED ON COMPARTMENT-SPECIFIC BIOLOGICAL FEATURES , 2006 .

[55]  Paul Horton,et al.  PROTEIN SUBCELLULAR LOCALIZATION PREDICTION WITH WOLF PSORT , 2005 .

[56]  W. Sung,et al.  Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines , 2005 .

[57]  Vladimir N. Vapnik,et al.  The Nature of Statistical Learning Theory , 2000, Statistics for Engineering and Information Science.

[58]  K. Chou,et al.  Prediction of protein structural classes. , 1995, Critical reviews in biochemistry and molecular biology.

[59]  Judith Klein-Seetharaman,et al.  PROTEINS: Structure, Function, and Bioinformatics 58:955–970 (2005) Protein Classification Based on Text Document Classification Techniques , 2022 .