LOC3D: annotate sub-cellular localization for protein structures.
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 three-dimensional (3D) structure. Localization is predicted using four different methods: (i) PredictNLS, prediction of nuclear proteins through nuclear localization signals; (ii) LOChom, inferring localization through sequence homology; (iii) LOCkey, inferring localization through automatic text analysis of SWISS-PROT keywords; and (iv) 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 >8700 eukaryotic protein chains taken from the Protein Data Bank (PDB). The web server can be used to predict sub-cellular localization for proteins for which only a predicted structure is available from threading servers. This makes the resource of particular interest to structural genomics initiatives.
Nair
Rajesh
R
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. nair@cubic.bioc.columbia.edu
Rost
Burkhard
B
D000818:Animals; D030562:Databases, Protein; D005057:Eukaryotic Cells / Q000737:chemistry; D020407:Internet; D016571:Neural Networks, Computer; D019913:Nuclear Localization Signals; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis* / Q000737:chemistry* / Q000502:physiology; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D014584:User-Computer Interface
D019913:Nuclear Localization Signals; D011506:Proteins