Nucleic Acids Research, 2003, Vol. 31, No. 13 3337-3340
© 2003 Oxford University Press
LOC3D: annotate sub-cellular localization for protein structures
1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA 2 Department of Physics, Columbia University, 538 West 120th Street, New York, NY 10027, USA 3 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue 4 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
*To whom correspondence should be addressed at CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. Tel: +1 2123054018; Fax: +1 2123057932; Email: nair{at}cubic.bioc.columbia.edu
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. Atalay and R. Cetin-Atalay Implicit motif distribution based hybrid computational kernel for sequence classification Bioinformatics, April 15, 2005; 21(8): 1429 - 1436. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Rost, G. Yachdav, and J. Liu The PredictProtein server Nucleic Acids Res., July 1, 2004; 32(suppl_2): W321 - W326. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Nair and B. Rost LOCnet and LOCtarget: sub-cellular localization for structural genomics targets Nucleic Acids Res., July 1, 2004; 32(suppl_2): W517 - W521. [Abstract] [Full Text] [PDF]
|
|