※The products of the CUCKOO Workgroup:
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.
(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
(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.
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.
(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.
(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.
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.
(2) CSS-Palm 1.0: The old version of CSS-Palm software.
(3) NBA-Palm 1.0: Another online predictor for S-palmitoylation site prediction, implementated in Naive Bayesian Algorithm.
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.
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.
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.
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.
(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.