1. Q: How to use GPS-PDeS 1.0 webserver?

A: You can obverse the latest version of GPS-PDeS 1.0 at download. We provide this tool on the website now, the software version will be uploaded after the paper was submitted. You can input the sequence of the protein you want to predict(in FASTA format), and choose the family/group information in the left menu. The result of predication will be showed soon.

2. Q: How to read GPS-PDeS 1.0 results?

A: Here we use the human p53 protein as the example. After clicking "Submit", the prediction results will be shown as follows:

<1>. The table of the GPS-PDeS 1.0 results (Page 1)

ID/name: The ID of the protein suquence which you input to predict

Peptide: The predicted dephosphorylation peptide with 7 amino acids upstream and downstream around the modified residue.

Position: The position of the site in the protein sequence.

Depho-type: The dephosphorylation type on this site.

Score: The value calculated by out GPS algortihm to estimate the potential of dephosphorylation. The higher the value is, the more potential the residue can be modified by phosphatase.

Cut-off: The cutoff value under the threshold you choose. Different threshold means different precision, sensitivity and specificity.

3. Q: Is GPS-PDeS 1.0 accurate?

A: Yes but not absolutely. Prediction of type-specific dephosphorylation sites is a not a easy job and now few people have enough understanding about it. The predication will be more accurate as the training data become abundant. But the training dataset now is very limited, especially compared with the phosphorylation information. We will still try to make the algorithm better and more powerful.However, our GPS-PDeS is the most impeccable and accurate tool on the dephosphorylation predication field now.

4. Q: How to choose the cut-off values and the thresholds?

A: The three thresholds of GPS-PDeS 1.0 were decided based on calculated Specificity. For all dephosphorylated types, the high, medium and low thresholds were established with specificity of 96%, 91% and 85%. The high threshold was designed for ocassions with strict requirement for false positive ratio. And the medium threshold relaxed the stringency to be useful in small-scale experiments. Also, the low threshold reduced the Sp to improve Sn considerably to be useful in exhaustively experimental identifying all potential methylated sites.

5. Q: What's the meaning of Specificity (Sp)? How do you calculate cutoff based on Sp?

A: Specificity (sometimes called the true negative rate) measures the proportion of negatives which are correctly identified as such (e.g the percentage of healthy people who are correctly identified as not having the condition). If we got 1000 negtive sites and 1000 positive sites and we want cutoff score while sp=0.9, we calculate the cutoff following these principles:

• (1) Calculated similarity scores for all positive and negative sites.
• (2) Sort all scores, increase cutoff from 0, until similarity scores of 90% of negative sites are below cutoff.
• (3) We got the cutoff we want.

6. Q: I have thousands of proteins for prediction, what should I do?

A:  For a large-scale prediction, we are so sorry that the software version is still under developed, and the webserver’ features is limited. We will try our best to finish the development of the tool's software.

7. Q:  I have a few questions which are not listed above, how can I contact the authors of GPS-PDeS 1.0?

A:  Please contact the three major authors: Weijia Zang, Chenwei Wang, and Dr. Yu Xue for details.