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

Keywords

Biology, Computational biology, Subcellular localization, Source code, Probabilistic logic

References

• Expert system for predicting protein localization sites in gram‐negative bacteriaKenta Nakai, Minoru Kanehisa — 1991
• The HMMTOP transmembrane topology prediction serverMiguel Casino Rubio — 2001
• Signals for protein targeting into and across membranes.Gunnar von Heijne — 1994
• Protein sorting signals and prediction of subcellular localization.Kenta Nakai — 2000
• The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000Amos Bairoch, Rolf Apweiler — 2000
• PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization.Kenta Nakai, Kenta Nakai, Paul Horton — 1999
• Using neural networks for prediction of the subcellular location of proteins.Anita Reinhardt — 1998
• The SWISS-PROT protein sequence data bank and its supplement TrEMBLAmos Bairoch, Rolf Apweiler — 1997
• Wanted: subcellular localization of proteins based on sequence.Frank Eisenhaber, Peer Bork — 1998
• Extensive feature detection of N-terminal protein sorting signalsHideo Bannai, Yoshinori Tamada, Osamu Maruyama — 2002
• Membrane protein biogenesis: the exception explains the rules.Harris D. Bernstein — 1998
• The PROSITE database, its status in 2002Laurent Falquet — 2002
• Predicting Protein Subcellular Localisation From Amino Acid Sequence InformationOlof Emanuelsson — 2002
• Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.Olof Emanuelsson, Henrik Nielsen, Søren Brunak — 2000
• A comparison of signal sequence prediction methods using a test set of signal peptidesKerstin M. L. Menne, Henning Hermjakob, Rolf Apweiler — 2000
• Principles governing amino acid composition of integral membrane proteins: application to topology prediction.Gábor Tusnády, István Simon — 1998
• Support vector machine approach for protein subcellular localization predictionSujun Hua, Zhirong Sun — 2001
• Sequence conserved for subcellular localizationRajesh Nair, Burkhard Rost — 2002
• Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.Henrik Nielsen, Jacob Engelbrecht, Søren Brunak — 1997
• The PROSITE database, its status in 1999Kay Hofmann, Philip Bucher, Laurent Falquet — 1999

Cited by

• Evidence for a copper-dependent iron transport system in the marine, magnetotactic bacterium strain MV-1.Michael Brenner, Markus Garschhammer, Friederike Nickl — 2004
• Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes.Dawn E. Holmes, Tünde Mester, Regina A. O'Neil — 2008
• FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures秀輝 渡辺, 秀樹 渡瀬, 登 伏見 — 2010
• Computer aided selection of candidate vaccine antigensR. A. Zakhidov, A. A. Vainer — 2010
• Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens.Muktak Aklujkar, Maddalena V. Coppi, Ching Leang — 2013
• Computational Approaches To Anti-Toxin Therapies And Biomarker IdentificationRebecca Swett — 2013
• Genómica funcional de Bordetella pertussis , implicancias sobre una enfermedad considerada reemergenteMaría Emilia Gaillard — 2009
• Les Patatines de Pseudomonas Aeruginosa : secrétées ou non secrétées ? Telle est la question ...Richard Salacha — 2010
• Protein Targeting ProtocolsMark van der Giezen — 2007
• Protein subcellular localization prediction using artificial intelligence technology.Rajesh Nair, Burkhard Rost — 2008
• Prokaryotic protein subcellular localization prediction and genome-scale comparative analysisNancy Yu — 2011
• Decision making based on association rulesSenqiang Zhou — 2006
• SpeB–Spi: a novel protease–inhibitor pair from Streptococcus pyogenesTodd F. Kagawa, Paul W. O’Toole, Jakki C. Cooney — 2005
• Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machinesJiren Wang, Wing‐Kin Sung, Arun V. Krishnan — 2005
• Genome-scale prediction of protein subcellular location in bacteria, with focus on extracellular and surface-associated proteins.Miaomiao Zhou — 2011
• Characterisation of bacteriophages that infect AcaryochlorisYi‐Wah Chan — 2010
• Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotationDwayne A. Elias, Aindrila Mukhopadhyay, Marcin P. Joachimiak — 2009
• Clonagem e expressão gênica de antígenos candidatos vacinais contra leptospirose.Vivian Lika Hashimoto — 2012
• Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chainsAlla Bulashevska, Roland Eils — 2006
• Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.Paola Gomez‐Pereira, Margarete Schüler, Bernhard M. Fuchs — 2012

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