LOC3D: annotate sub-cellular localization for protein structures

Rajesh Nair1, Burkhard Rost2
1nair@cubic.bioc.columbia.edu, Columbia University; 2rost@columbia.edu, Columbia University

LOC3D (http://cubic.bioc.columbia.edu/db/LOC3D/) is both a weekly-updated database and a web server for predictions of sub-cellular localization for eukaryotic proteins of known structure. Localization is predicted using four different methods: (1) PredictNLS: prediction of nuclear proteins through nuclear localization signals, (2) LOChom: inferring localization through sequence homology, (3) LOCkey: inferring localization through automatic text analysis of SWISS-PROT keywords, and (4) and LOC3Dini: ab initio prediction through a system of neural networks and vector support machines. The final prediction is based on the method that predicts localization with the highest confidence. The LOC3D database currently contains predictions for over 8700 eukaryotic protein chains taken from PDB. The web server can be used to predict sub-cellular localization for proteins for which only a predicted secondary structure is available. This makes the resource of particular interest to structural genomics initiatives. LOC3D has been used to annotate sub-cellular localization for six entirely sequenced eukaryotic genomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae).