Protein Localization Database for Human and Arabidopsis

 
 
 

Please cite:

Nucleic Acids Res. 2011 Jan;39(Database issue):D230-4. PubMed PMID: 21071420.

References:

Some experimental datasets:

Arabidopsis thaliana (Weed)

1: Zybailov B et. al. PLoS ONE. 2008 Apr 23;3(4):e1994. PubMed PMID: 18431481.

2: Marmagne A et.al. Mol Cell Proteomics. 2007 Nov;6(11):1980-96. PubMed PMID: 17644812.

3: Benschop JJ et. al. Mol Cell Proteomics. 2007 Jul;6(7):1198-214. PubMed PMID: 17317660.

4: Jaquinod M et.al. Mol Cell Proteomics. 2007 Mar;6(3):394-412. PubMed PMID: 17151019.

5: Dunkley TP et. al. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6518-23. PubMed PMID: 16618929.

Homo sapiens (Human)

1: Anderson NL et. al. Mol Cell Proteomics. 2004 Apr;3(4):311-26. PubMed PMID: 14718574.

2: Calvo S et. al. Nat Genet. 2006 May;38(5):576-82. PubMed PMID: 16582907.

3: Leung AK et. al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D218-20. PubMed PMID: 16381850.

4: Sheng S et. al. Mol Cell Proteomics. 2006 Jan;5(1):26-34. PubMed PMID: 16188874.

5: Gassmann R et. al. Chromosoma. 2005 Feb;113(7):385-97. PubMed PMID: 15609038.

Some published databases:

1: LOCATE: A mammalian protein subcellular localization Database. Sprenger J et.al. Nucleic Acids Res. 2008 Jan;36(Database issue):D230-3. PubMed PMID: 17986452.

2: MitoP2: The Mitochondrial Proteome Database. Elstner M et.al. Methods Enzymol. 2009;457:3-20. PubMed PMID: 19426859.

3: NPD: The Nuclear Protein Database. Dellaire G et.al. Nucleic Acids Res. 2003 Jan 1;31(1):328-30. PubMed PMID: 12520015.

4: HPRD: A Human Protein Reference Database. Prasad T et.al. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72. PubMed PMID: 18988627.

5: SUBA: the Arabidopsis Subcellular Database. Heazlewood JL. et. al. Nucleic Acids Res. 2007 Jan;35(Database issue):D213-8. PubMed PMID: 17071959.

Links:

Useful links for Prediction Methods:

LOCtree: Nair R, Rost B. J Mol Biol. 2005 Apr 22;348(1):85-100. PubMed PMID: 15808855. Server: http://cubic.bioc.columbia.edu/services/LOCtree/

TargetP: Emanuelsson O et. al. J Mol Biol. 2000 Jul 21;300(4):1005-16. PubMed PMID: 10891285. Server: http://www.cbs.dtu.dk/services/TargetP/

WOLFPSORT: Horton P et. al. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7. PubMed PMID: 17517783. Server: http://wolfpsort.org/

MultiLoc: Hoeglund A et. al. Bioinformatics. 2006 May 15;22(10):1158-65. PubMed PMID: 16428265. Server: http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc/

PredictNLS: Cokol M et. al. EMBO Rep. 2000 Nov;1(5):411-5. PubMed PMID: 11258480. Server: http://www.rostlab.org/services/predictNLS/

NucPred: Brameier M et. al. Bioinformatics. 2007 May 1;23(9):1159-60. PubMed PMID: 11258480. Server: http://www.sbc.su.se/~maccallr/nucpred/

 

Resources:

TAIR : The Arabidopsis Information Resource
Ensembl : The Ensembl project produces genome databases
UniProtKB : Protein knowledgebase
Gene Ontology : The Gene Ontology project

 

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The basic protein targeting pathways
Click to see the list of all proteins.
 

 

 

 
© Copyright 2008 RostLab. All Rights Reserved. Shruti Rastogi (locdb@rostlab.org)