Tutorial in Search Page
Step 1. User can easily search three major queries involving Protein keyword (Protein name or Gene Name), or Database ID (SwissProt ID, SwissProt AC, GO ID, or InterPro ID), or Protein Sequence (in FASTA format) in the search page. Firstly, users fill the input data corresponding to your interesting fields and then click on the "Submit" button to query the matching proteins.
Step 2. After a while, the proteins matching the query keywords are retrieved from our database and shown in a table. To view the detailed information about the protein (such as protein function, PTM sites, protein domain, etc.), users just click on the URL link "show".
Step 3. The detail information about PTM are displayed in this page. The experimental and predicted PTM sites are described in both tabular and graphical visualizations. User could exploit more concerning things such as solvent accessibility of the residues, protein variations, protein secondary structure and protein functional domain in "Overview of Protein Modification site with Functional and Structural Information"
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 was created to facilitate the investigation in each type of PTM. Total five summary tables are designed to support for users to browse all the types of PTM in the release 2016 of dbPTM. In the tables, each type of PTM was categorized by their modified amino acids with the number of experimentally verified sites. For example, users can choose the phosphorylation of Serine (S) 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 get more detailed information phosphorylation of Serine (S), 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 substte 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 also provided.