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. Prediction of protein S-nitrosylation.

(1) GPS-SNO 1.0: computational prediction of protein S-nitrosylation sites with GPS 3.0 algorithm.

Website: http://sno.biocuckoo.org/

8. Prediction of tyrosine nitration.

(1) GPS-YNO2 1.0: The first computational program for computational prediction of tyrosine nitration sites in proteins with GPS 3.0 algorithm.

Website: http://yno2.biocuckoo.org/

9. Prediction of calpain cleavage sites.

(1) GPS-CCD 1.0: A novel computational program for the prediction of calpain cleavage sites with GPS 2.1 algorithm.

Website: http://ccd.biocuckoo.org/

10. Prediction of pupylation sites.

(1) GPS-PUP 1.0: The first computational program for computational prediction of pupylation sites in prokaryotic proteins with GPS 2.2 algorithm.

Website: http://pup.biocuckoo.org/

11. Databases.

(1) MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

Website: http://microkit.biocuckoo.org

(2) PhosSNP 1.0: systematic analysis of genetic polymorphisms that influence protein phosphorylation.

Website: http://phossnp.biocuckoo.org/

(3) CPLA 1.0: an integrated database of protein lysine acetylation.

Website: http://cpla.biocuckoo.org/

(4) THANATOS 1.0: an integrated database of cell death related proteins.

Website: http://thanatos.biocuckoo.org/

12. 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/