1. ExPASy: A proteomics server of the Swiss Institute of Bioinformatics (SIB) which analyzes protein sequences and structures and two-dimensional gel electrophoresis (2-D Page electrophoresis). The server functions in collaboration with the European Bioinformatics Institute. ExPASy also produces the protein sequence knowledgebase, UniProtKB/Swiss-Prot, and its computer annotated supplement, UniProtKB/Trembl.
2. Phospho.ELM: The best public database for phosphorylation sites. The current version of Phospho.ELM is 7.0.
3. GPS 2.0: A kinase-specific phosphorylation sites predictor. Previously, we designed a novel algorithm of GPS (Group-based Phosphorylation sites Prediction) and release GPS 1.10. Recently, we greatly improved the GPS algorithm and renamed the GPS as Group-based Prediction System.
4. PPSP 1.0: We also developed another online program for prediction of kinase-specific phosphorylation sites, implemented in Baysian Decision Theory (BDT).
5. SUMOsp 2.0: Prediction of protein sumoylation sites. The current version of SUMOsp program.
6. SSP 1.0: 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.
7. CSS-Palm 2.0: Prediction of protein palmitoylation sites. The current version of CSS-Palm program.
8. NBA-Palm 1.0: Previously, we also developed an alternative predictor for palmitoylation sites prediction. Several machine learning algorithms, such as Naive Bayesian, SVMs (Support Vector Machines) and Artificial Neural Network (RBF), were employed and compared. Finally, the Naive Bayesian algorithm (NBA) was used for its outstanding performance.
9. PAIL 1.0: Prediction of protein acetylation sites. We used a Bayesian algorithm to construct a predictor.
10. MeMo 2.0: Methylation Modification Prediction Server. We used the SVMs algorithm to develop a online tool for protein methylation sites prediction.