※ User Guide:
This website is free and open to all users and there is no login requirement.Tutorial:
Frequently Asked Questions:
1. Q: How to use GPSD webserver?
A: First, you could find the prediction website in "WEB SERVER" page of GPSD. Second, enter protein sequence(s) in fasta format, which starts with a '>' followed with protein/peptide name. Then, select the phosphatase node(s). The predictor contains 9 S/T families and 3 Y families for phosphatases. Just click the "Submit" button, wait a moment, you can get the prediction results of phosphatase-specific dephosphorylation sites on substrate.
2. Q: How to read the GPSD results?
A:
Here we use the human protein TP53 as the example. After clicking "Submit", the prediction results of PPP2CA-catalyzed sites with high threshold are shown as follows:
ID: The name/id of the protein sequence that you input to predict. Position: The position of the site which is predicted to be dephosphorylated. Code: The residue which is predicted to be dephosphorylated. Phosphatase: The regulatory phosphatase which is predicted to dephosphorylate the site. Peptide: The predicted dephosphopeptide with 7 amino acids upstream and 7 amino acids downstream around the modified residue. Score: The value calculated by GPSD algorithm to evaluate the potential of dephosphorylation. The higher the value, the more potential the residue is dephosphorylated. Cutoff: The cutoff value under the threshold. Different threshold means different precision, sensitivity and specificity. Source: Whether this dephosphorylation site validated by experiment, "Exp." means YES, while "Pred." means NO. "Exp." links to the source site. Interaction: Whether the interaction between this substrate and this phosphatase validated by BioGrid, "√" that links to the source PubMed page, means YES, while "--" means NO. Logo: The sequence logo of this dephosphopeptide. Part 1: Part 2: 3.
Q: How to choose the cut-off values and the thresholds? A:
Firstly, we calculated the theoretically maximal
false positive rate (FPR) for each PPP cluster.
The three thresholds of GPSD were decided based
on calculated FPRs.For serine/threonine phosphatases,
the high, medium and low thresholds were established
with FPRs of 2%, 6% and 10%. And for tyrosine
phosphatases, the high, medium and low thresholds were
selected with FPRs of 5%, 10% and 15%.
4.
Q: I have a few questions which are not listed above, how can I contact the authors of GPSD? A:
Please contact the major author: Cheng Han, Shanshan Fu, Dr. Di Peng, and Dr.
Yu Xue for details. 5. Q:
Can I use GPSD on different browsers?
A: Yes, we tested our web server on different browsers.
<1>. The table of the GPSD results
<2>. The visualization of default prediction
Up: The visualization for the positional distribution of the predicted site in protein sequence. By default, the sites with the highest 3 predicted scores are displayed.
Down: The visualization for protein disordered region predicted by IUPred
[PMID: 15955779]. Cutoff = 0.5, if score of prediction > cutoff, the residue is considered in disordered region.
Left: The distribution of S/T/Y sites in phosphatase families.
The distribution of S/T/Y sites.
The distribution of S/T/Y sites in disordered region.
OS Version Chrome Firefox Microsoft Edge Safari Linux Ubuntu 20.04 127.0.6533.119 129.0.1 N/A N/A MacOS 14.1 127.0.6533.120 129.0.1 N/A 17.1 Windows 10 127.0.6533.120 129.0.1 127.0.2651.98 N/A