Tutorial in Search Page

Step 1. Three major queries in search page. Users can query their interested protein by input the protein name, gene name, Swiss-Prot ID or AC in search field of homepage. It was also allowed the users to query the amino acid sequence against the release 53.0 of Swiss-Prot protein sequences.

Step 2. The search result. Since users input the keyword of protein name or gene name, Swiss-Prot ID or AC in search field of homepage. The proteins matching the query keywords were shown in a table. Then, users can click on the URL link "show" to view the detailed information about the protein, such as protein function, PTM sites, protein doamin, etc.

Step 3. The detail information about PTM. Users can view the experimental and predicted PTM sites in both tabular and graphical visualizations. Graphical visualization could reveal an overview of the post-translational modification sites, the solvent accessibility of the residues, protein variations, protein secondary structures and protein functional domains in protein sequence.

Step 4. The orthologous conserved regions. Users can investigate whether a PTM site located in orthologous conserved regions by click on the button "show" in the table of PTM sites.

Tutorial in Browse Page

Step 1. The summary table of PTMs. To facilitate the investigation in each type of PTM, we developed a summary table for users to browse all the types of PTM in the release 2.0 of dbPTM. In the table, each type of PTM was categorized by their modified amino acids with the number of experimentally verified sites. For example, users can choose the acetylation of lysine (K) to take the more detailed information such as the position of modification on amino acid, the location of modification on protein sequence, the modified chemical formula, and the mass difference.

Step 2. Users can investigate the detailed information acetylation of lysine (K), such as the position of modification on amino acid, the location of modification on protein sequence, the modified chemical formula, and the mass difference. Especially, the formula structure was visualized by the Jmol program which was implemented in JAVA Applet. However, the most effective knowledge about the PTM is the substrate site specificity including the frequency of amino acids, the average solvent accessibility, and the frequency of secondary structure surrounding the modified site. The sequence logo which represents the frequency of amino acids and the frequency of secondary structure surrounding the modified sites was provided.