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Title | LOC3D: annotate sub-cellular localization for protein structures. |
Publication Type | Journal Article |
Year of Publication | 2003 |
Authors | Nair, R, Rost, B |
Journal | Nucleic Acids Res |
Volume | 31 |
Issue | 13 |
Pagination | 3337-40 |
Date Published | 2003 Jul 1 |
ISSN | 1362-4962 |
Keywords | Animals, Databases, Protein, Eukaryotic Cells, Internet, Neural Networks (Computer), Nuclear Localization Signals, Protein Conformation, Proteins, Sequence Analysis, Protein, Sequence Homology, Amino Acid, User-Computer Interface |
Abstract | 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 Journal | Nucleic Acids Res. |
PubMed ID | 12824321 |
PubMed Central ID | PMC168921 |