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INTRODUCTION:
The
past decade has witnessed the rapid progresses
on functional dissections of protein sumoylation
(Geiss-Friedlander
and Melchior, 2007). The SUMO (small
ubiquitin-related modifier) gene SMT3 was firstly
identified in S. cerevisiae as a suppressor
of the centromeric protein Mif2 (Meluh
and Koshland, 1995), and later was
shown to be covalently coupled to the Ran GTPase-activating
protein RanGAP1 as a reversible modifier (Mahajan,
et al., 1997; Matunis,
et al., 1996). Proteins modified
by SUMO could alter their sub-cellular localization,
activity or stability, etc (Fernandez-Lloris,
et al., 2006; Mahajan,
et al., 1997; Matunis,
et al., 1996). And protein sumoylation
plays important roles in a variety of biological
processes, such as transcriptional regulation,
signaling transduction, cell cycle progression
and differentiation (Deyrieux,
et al., 2007; Gill,
2004; Montpetit,
et al., 2006; Seeler
and Dejean, 2003), etc. In addition,
aberrance of SUMO system is highly implicated
in numerous diseases and cancer developments
(Dorval
and Fraser, 2007; Fernandez-Lloris,
et al., 2006; Li,
et al., 2005; Seeler,
et al., 2007).
In this work,
we updated our SUMOsp
1.0 into version 2.0.
The training data set was manually collected from scientific
literature. The non-redundant training data contained
279 sumoylation sites from 166 distinct proteins. Then
an updated version of GPS algorithm was deployed. The
self-consistency, leave-one-out validation and 4-, 6-,
8-, 10-fold cross-validations were calculated to evaluate
the prediction performance and system robustness of
SUMOsp 2.0. Also, the prediction performance was tested
on an additional data set not included in the training
data set, with 53 sumoylation sites from 31 proteins.
We compared SUMOsp 2.0 with SUMOplot and SUMOsp 1.0,
on both the training data and new data. The specificity
(Sp) of SUMOsp 2.0 was improved significantly, while
the sensitivity (Sn) was similar or just slightly reduced
against previous tools. The SUMOsp 2.0 was implemented
in JAVA 1.4.2 and would
use local CPU for computation. With a high speed, SUMOsp
2.0 could predict out potential sumoylation sites for
~1,000
proteins (with an average length of ~1000aa) within
ten minutes. Taken together, we proposed that the highly
specific SUMOsp 2.0 web server will be more efficient
for sumoylation sites prediction. The SUMOsp 2.0 is
freely available at: http://sumosp.biocuckoo.org.
This
website is linked in ExPASy
Proteomics Tools page.

SUMOsp
2.0 User Interface
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