LOC3D: annotate sub-cellular localization for protein structures.

TitleLOC3D: annotate sub-cellular localization for protein structures.
Publication TypeJournal Article
Year of Publication2003
AuthorsNair, R, Rost, B
JournalNucleic Acids Res
Date Published2003 Jul 1
KeywordsAnimals, Databases, Protein, Eukaryotic Cells, Internet, Neural Networks (Computer), Nuclear Localization Signals, Protein Conformation, Proteins, Sequence Analysis, Protein, Sequence Homology, Amino Acid, User-Computer Interface

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.

Alternate JournalNucleic Acids Res.
PubMed ID12824321
PubMed Central IDPMC168921