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Nucleic Acids Research, 2003, Vol. 31, No. 1 397-399
© 2003 Oxford University Press

NLSdb: database of nuclear localization signals

Rajesh Nair*,1,2, Phil Carter1 and Burkhard Rost1,3,4

1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, BB217, 650 West 168th Street, New York, NY 10032, USA 2 Department of Physics, Columbia University, 538 West 120th Street, New York, NY 10027, USA 3 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA 4 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, BB217, 650 West 168th Street, New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 212 305 3773; Fax: +1 212 305 7932; Email: nair{at}cubic.bioc.columbia.edu

ABSTRACT

NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using ‘in silico mutagenesis’ this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. NLSdb can be accessed via the web site: http://cubic.bioc.columbia.edu/db/NLSdb/.


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