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 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 databases.The database also contains over 12500 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-localise 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/.
Thanks to Jinfeng Liu (Columbia University)for computer assistance and the collection of genome data sets;to Jinfeng Liu and Dariusz Przybylski (Columbia University)for providing preliminary information and programs.PC and BR were supported by the grant 1-P50- GM62413-01 from the National Institute of Health (NIH);RN and BR were supported by the grant DBI-0131168 from the National Science Foundation (NSF).Last,not least,thanks to Amos Bairoch (SIB,Geneva)and Rolf Apweiler (EBI,Hinxton)and their crews for maintaining excellent databases and to all experimentalists without whom we could not have built our database.
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