Submit Phosphoprotein tab:
The user should paste a single or multiple protein sequences (max 10) in FASTA format in the first input field. In the second input field, a corresponding list of mapped phosphorylation sites should be pasted in or uploaded in the format seen in the example. It is possible to include the known phosphorylation sites from the databases phospho.ELM (http://phospho.elm.eu.org/) and phosphoSite (http://www.phosphosite.org/). By default an example is always provided when [Phospho Sites Confirmation] tab is selected; use [Clear Fields] button to clear the fields to paste in your own sequences.
Once the above configuration has been settled, the user should click [Phospho Sites Confirmation] and the requested phosphosites and positions in the proteins will be verified. This is useful when mistakes are made (marked with question marks), for example when a wrong phosphorylation position is attributed to an amino acid other than S/T/Y. It is possible to [Go Back] and correct the phosphosites if these are not positioned correctly.
After this phosphosite verification, the web service starts the NetPhorest classification when the [Get NetPhorest Classifications] button is clicked. After a few moments the results are generated and displayed in a tabular form, in which each protein can be viewed by the "fold out" button. Besides listing relevant information such as the position, the type of phosphoacceptor residue and the peptide surrounding the phosphosite, the table lists the "Posterior Probability" score. This score indicates the probability that a phosphosite is a substrate of a particular kinase (KIN) or phospho-binding domain (SH2 or PTB). The scores for the individual phosphosites are sorted so the most probable is listed first. Users can download the results in a "tab-separated-values" (.tsv) format.
