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PEDS Advance Access published online on November 10, 2007
Protein Engineering Design and Selection, doi:10.1093/protein/gzm057
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM

Hong-Bin Shen1,2,4,5 and Kuo-Chen Chou1,3

1 Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 1954 Hua-Shan Road, Shanghai 200030, China 2 School of Information Engineering, Jiangnan University, Wuxi 214122 3 Gordon Life Science Institute, San Diego, CA 92130, USA

5 To whom correspondence should be addressed.E-mail: hbshen{at}crystal.harvard.edu

The life processes of an eukaryotic cell are guided by its nucleus. In addition to the genetic material, the cellular nucleus contains many proteins located at its different compartments, called subnuclear locations. Information of their localization in a nucleus is indispensable for the in-depth study of system biology because, in addition to helping determine their functions, it can provide illuminative insights of how and in what kind of microenvironments these subnuclear proteins are interacting with each other and with other molecules. Facing the deluge of protein sequences generated in the post-genomic age, we are challenged to develop an automated method for fast and effectively annotating the subnuclear locations of numerous newly found nuclear protein sequences. In view of this, a new classifier, called Nuc-PLoc, has been developed that can be used to identify nuclear proteins among the following nine subnuclear locations: (1) chromatin, (2) heterochromatin, (3) nuclear envelope, (4) nuclear matrix, (5) nuclear pore complex, (6) nuclear speckle, (7) nucleolus, (8) nucleoplasm and (9) nuclear promyelocytic leukaemia (PML) body. Nuc-PLoc is featured by an ensemble classifier formed by fusing the evolution information of a protein and its pseudo-amino acid composition. The overall jackknife cross-validation accuracy obtained by Nuc-PLoc is significantly higher than those by the existing methods on the same benchmark data set through the same testing procedure. As a user-friendly web-server, Nuc-PLoc is freely accessible to the public at http://chou.med.harvard.edu/bioinf/Nuc-PLoc.

Keywords: fusion/Nuc-PLoc/position-specific scoring matrix/pseudo-amino acid composition/subnuclear location

Received July 16, 2007; revised August 13, 2007; accepted September 13, 2007.

4 Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA


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