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1.
Prediction of phosphorylation sites.
(1)
GPS
2.1 (Group-based
Prediction System): One of our recent projects.
We improved our previous GPS (Group-based Phosphorylation
scoring) algorithm and released GPS 2.0 & GPS
2.1 algorithm. The GPS 2.0 (Group-based Prediction
System, ver 2.0) software was implemented in JAVA
and could predict kinase-specific phosphorylation
sites for 408
human PKs in hierarchy. Recently, we released GPS
2.1 with a novel Peptide Selection method to improve
the prediction performance and robustness greatly.
Website: http://gps.biocuckoo.org/
(2)
GPS
1.1 (Group-based
Phosphorylation scoring): In 2004 & 2005, we
designed a novel algorithm GPS and construct an
easy-to-use web server for the experimentalists.
GPS 1.1 could predict kinase-specific phosphorylation
sites for 71
PK groups with 216
unique PKs
Website: http://gps.biocuckoo.org/1.1/
(3)
PPSP
1.0 (Prediction of PK-Specific Phosphorylation site):
The software was implemented in Bayesian Decision
Theory (BDT) algorithm. The prediction performance
is comparable with GPS 1.1.
Website: http://ppsp.biocuckoo.org/
2.
Prediction of SUMO substrates & sumoylation
sites.
(1)
SUMOsp
2.0 (SUMOylation sites prediction): One of our recent
projects. An enhanced software for prediction of
sumoylation site, with GPS 2.0 algorithm.
Website: http://sumosp.biocuckoo.org/
(2)
SUMOsp
1.0 (SUMOylation sites prediction): The old version
of SUMOsp software, which was implemented in GPS
1.1 algorithm and Motif-X
method.
Website: http://sumosp.biocuckoo.org/1.0/
(3)
SSP 1.0
(SUMO Substrates Prediction): A genome-wide analysis
of sumoylation-related biological processes and
functions in human nucleus. Totally 2,683 potential
SUMO substrates conserved in both human and mouse
were identified. And we design a simple query software
to search the results.
Website: http://ssp.biocuckoo.org/
3.
Prediction of palmitoylation sites.
(1)
CSS-Palm
2.0: One of our recent projects. We used GPS 2.0
algorithm to develop CSS-Palm 2.0.
Website: http://csspalm.biocuckoo.org/
(2)
CSS-Palm
1.0: The old version of CSS-Palm software.
Website: http://csspalm.biocuckoo.org/1.0/
(3)
NBA-Palm
1.0: Another online predictor for S-palmitoylation
site prediction, implementated in Naive Bayesian
Algorithm.
Website: http://nbapalm.biocuckoo.org/;
http://www.bioinfo.tsinghua.edu.cn/NBA-Palm/
4.
Prediction of protein methylation sites.
(1)
Memo
2.0: The first computational program for prediction
of protein methylation site on either lysine or
arginine residues. The Memo 2.0 was implemented
in SVMs (support vector machines) algorithm.
Website: http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html
5.
Prediction of acetylation sites.
(1)
PAIL 1.0: The first computational
program for prediction of protein acetylation sites
on internal lysines. The PAIL 1.0 was implemented
in BDM (Bayesian Discriminant Method) algorithm.
Website: http://bdmpail.biocuckoo.org/
6.
Prediction of ubiquitination sites.
(1) BDM-PUB
1.0: The first computational program for prediction
of protein ubiquitination sites. The BDM-PUB 1.0 was
implemented in BDM (Bayesian Discriminant Method)
algorithm.
Website: http://bdmpub.biocuckoo.org/
7.
Miscellaneous tools.
(1) DOG
1.0 (Domain Graph): It could be used to prepare publication-quality
figures of protein domain structures. The scale of
a protein domain and the position of a functional
motif/site will be precisely calculated.
Website: http://dog.biocuckoo.org/
(2) PPS
1.0 (PTMs Peptide Scanner): It could be used to reveal
known or highly potential PTM sites in eukaryotic
proteins. Five typical PTMs were considered, including
phosphorylation, sumoylation, palmitoylation, methylation
and acetylation.
Website: http://pps.biocuckoo.org/
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Last update: Aug. 10th, 2010