Help  

The iProt-Sub webserver can be accessed at https://iProt-Sub.erc.monash.edu.au for the online prediction of protease substrates and their corresponding cleavage sites from primary amino acid sequences only. At present, iProt-Sub can predict the substrate cleavage sites for 40 different proteases involving aspartic (A), cysteine (C), metallo (M) and serine (S) protease superfamilies. Different from other general tools, iProt-Sub uses a machine learning approach based on support vector regression (SVR) to provide the real-valued prediction of substrate cleavage probability. In particular, it uses 11 different encoding schemes to extract the local sequence and structural profiles including AAC, ACC, AAindex, Binary, Blosum, CHR, CKSAAP, DISO, KNN, PSI and PSSM. This strategy has significantly improved the predictive performance of iProt-Sub and Cascleave, our previously established tool for predicting caspase substrate cleavage sites. The rationale behind this approach is that peptide sequences that can be cleaved by proteases should exhibit different features opposed to those that cannot be cleaved. Therefore, integrating the features encoded by multi-encoding schemems could principally provide more informaitve features than the conventional amino acid sequence encoding scheme.

1: Easy User Guide  

A three-step tutorial is shown below:

• star Paste the sequences in the text box in standard FASTA format. We allow users to paste up to 50 sequences per time. If you have large scale data for analysis, please contact us;
• star At least fill your email address in order to receive the result visualization link;
• star Submit your job to the server.

Figure 1. The user guide of iProt-Sub server.

2: Results Display and Analysis  

As shown in Figure 2, it is the Type-1 (DIAGRAM A) interactive and zoomable results visualization. Four types of proteases family are shown in different color. The long bar represents a substrate sequence with the many colorful lines (representing cleavage sites) showing on it. More detailed information will show within a box when the mouse point to the corresponding colorful line.

Figure 2. The Type-1 results visualization of iProt-Sub server.

Type-2 result visualization (DIAGRAM B) is shown in Figure 3. In this graphic, each cluster represents a protein sequence, and we use orange, green, red and purple nodes represent cleavage sites with the fragment information showing with. In this interactive diagram, each node can be drag and hold, double click to release the fixed nodes.

Figure 3. The Type-2 results visualization of iProt-Sub server.

Four Tabs can be seen in Figure 4, and the protease-specific and species-specific predicted cleavage sites are shown in a form below them. Each form contains the information: position of cleavage site, protein sequence ID, segment, N and C fragment as well as the predicted scores.

Figure 4. The protease-specific result forms of iProt-Sub server.

3: Citation  

Song J, Wang Y, Li F, et al., 2018, iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Submitted for publication

personContact  

iProt-Sub Development Team
Biomedicine Discovery Institute
Faculty of Medicine, Nursing and Health Sciences
Monash Centre for Data Science
Faculty of Information Technology
Monash University
Melbourne, VIC 3800, Australia