※ Documentation:

Data statistics and function for GPS-SUMO 2.0, GPS-SUMO, SUMOsp 2.0 and SUMOsp
ContentGPS-SUMO 2.0GPS-SUMOSUMOsp 2.0SUMOsp
Non-redundant Data Sets
Sumoylation Sites63,716912332239
SUMO Substrates9,731510197144
SIMs17613700
SUMO-interacting Proteins1048000
Species131296
Data Size~7.2 GB~30 MB~17 MB~10 MB
Algorithms and Functions
Features11111
SIM Predictor√√××
Species-specific Prediction√×××
PPI Pairs27,482×××
3D Structures6,428×××

Frequently Asked Questions:

1. Q: How to use GPS-SUMO 2.0 web server?

A: Please visit GPS-SUMO 2.0 at https://sumo.biocuckoo.cn/online.php. We provide 5 versions of prediction for users. You can click “here” at “WEB SERVER” page to change the online service mode or just click the following names of predictor:

(1) Online Service (Penalized Logistic Regression): The default web has fast speed and visualization function. We provide 3D structure, statistics and disorder propensity of protein.
(2) Online Service (Transformer Neural Network): The deep-learning prediction balances the accuracy with speed.
(3) Online Service of Comprehensive Prediction: The comprehensive prediction has all models and annotations of secondary structure and surface accessibility.
(4) Online Service of Species-specific Prediction: We provide 13 species for species-specific prediction. If you want to focus on certain species, you may choose this one.
(5) Online Service of Prediction According to Protein Identifier: If you want to predict with gene name, protein name or UniProt Accession, please choose this one.

For Windows and Unix/Linux users, please use the keyboard shortcuts "Ctrl+C & Ctrl+V" to copy and paste your FASTA format sequences into TEXT form for prediction. And for Mac users, please use the keyboard shortcuts "Command+C & Command+V". You could input one primary sequence or multiple proteins' sequences in FASTA format.

Then please click on the "Submit" button to run the program. The prediction results will be shown in the prediction form. Again, please click on the ‘Download’ button on the top of the prediction form to save the results in TXT, Excel or ZIP format. If you want to download statistical graphics, please click on the “Export” button.

2. Q: Is GPS-SUMO 2.0 much better than GPS-SUMO?

A: Yes! Firstly, the fourth-generation GPS (Group-based Prediction System) algorithm was remained in GPS-SUMO 2.0 and more sequence- and structure- based features and deep learning algorithm have been added. The prediction performance was greatly improved against our previous tools. Secondly, we updated options allowing users to predict with protein sequence or identifiers. We also provide the PPI information, sequence WebLogo, 3D structures, links to PTM database and prediction of secondary structure and disorder propensity. The visualization and user-friendless were greatly improved. Thirdly, the training data set of GPS-SUMO 2.0 was updated by searching the scientific literature published before June 2020 and 13 PTM databases, which is the largest amount of training data so far. Thus, the prediction accuracy of GPS-SUMO 2.0 was significantly improved.

3. Q: There are three thresholds used in your predictor, what do these parameters mean?

A: There are two types of predictors including sumoylation sites or SUMO-interacting motifs, the threshold options only affect the corresponding one. After GPS-SUMO 2.0 predictor model was well-trained, we performed an evaluation on this model. From the evaluation, three thresholds with high, medium and low stringencies were chosen for GPS-SUMO. The performance under these three thresholds was presented as follow:

The performance of GPS-SUMO in different threshold
  Sumoylation SUMO interaction
 
Ac Sn Sp MCC Pr Ac Sn Sp MCC Pr
High 76.16% 57.24% 95.08% 0.5652 92.08% 85.83% 67.50% 95.00% 0.6731 87.10%
Medium 78.75% 67.34% 90.16% 0.5906 87.25% 92.50% 97.50% 90.00% 0.8450 82.98%
Low 80.38% 75.76% 85.00% 0.6102 80.38% 90.00% 98.75% 85.62% 0.8046 77.45%

4. Q: I have a few questions which are not listed above, how can I contact the authors of GPS-SUMO 2.0?

A: Please contact the responding author: Dr. Yu Xue for details.

5. Q: Can I use GPS-SUMO 2.0 on different browser?

A: Yes, we test our web server on different browsers.

Browser compatibility
OSVersionChromeFirefoxMicrosoft EdgeSafari
LinuxUbuntu 18.04107.0.5304.107107.0.1N/AN/A
MacOSHighSierra107.0.5304.107107.0.1N/A13.1.2
Windows10107.0.5304.107107.0.1108.0.1462.46 N/A