1. Searching Database
Searching through PTMPDB is fairly straightforward. In PTMPDB, we have provided several search options to facilitate fast data retrieval from PTMPDB.
(1) Searching with Uniprot ID and Database ID.
6473 proteins documented in PTMPDB can be mapped to UniProt database. In ID search, two search methods are provided: search with UniProt ID and Database ID. UniProt ID is composed by 6 letters and digits, while Database ID is a consecutive number. In total, there are 10477 UniProts in PTMPDB.
(2) Searching with Keywords.
In addition, we also have provided search by protein name. Users can get example keywords by pressing "Example" button.
2. Overview of Protein and Structures
We used 3Dmol for the presentation and visualization of protein structure . You can enter the detailed information page to view the 3d structure.
3. Protein Sequence Alignment
We conducted blast against UniProt database for all the protein entries in PTMPDB and have extracted their alignment results. ALIGNMENT-TO-HTML (HTML-based interactive visualization for annotated multiple sequence alignments) was used to display the alignment results in PTMPDB (showed in the following figures).
You can view the alignment results in the detailed information page.
4. Disorder Picture
We provided disordered region prediction results from D2P2 database for each protein entry if it can be mapped to the UniProt database. A link to show larger figure is also provided in this section.
You can also select another UniProt belongs to the PDB chain to view.
If the thumbnail is not clear enough, you can open the full viewer by clicking the link below the thumbnail.
5. Protein Feature View
We provide a clearer visualization of protein sequences using the Protein Feature View. You can choose UniProt to view another feature.
6. Sequence Viewer
In addition, we use rcsb sequence viewer to show you the PDB information in a different way.
7. Mutation Information
We provide the mutation information associated with the PTMs.
You can find every update of our project and track prior data versions on the Timeline page.
You can also get access to the timeline page through the links in both home page and download page.
9. Submitting New Protein
On SUBMISSION webpage, users can submit their new proteins information. Each field marked with red asterisk is required. We will commence on submission request once we receive user’s submission and will contact the user if needed.