How to use CRHunter?
 
To predict catalytic residues, you need to conduct a six-step procedure as shown in the following figure: (1) Choose the type of submission; (2) Paste or upload your query protein file; (3) Select the query chain in your structural file (If you select structural model- or sequence-based prediction, please disregard this step); (4) Assign the sequence identity cutoff to remove the close homologs (Optional); (5) Input your email address for retrieving the results (Optional); (6) Click the submit button.


Once your job is successfully submitted, CRHunter will assign a Job ID to your query. You can check the running status and retrieve your results using this Job ID. Generally, the prediction process will be finished in 15 minutes for a single query. After the job is done, the URL of the results webpage will be returned to you by email.
 
Format of input file
 
CRHunter can be used to predict catalytic residues from both protein sequence and structure. If you select the structure-based prediction, please input the standard PDB format as shown in the following figure A. If you select the structural model- or sequence-based prediction, please input the standard FASTA format as shown in the following figure B. The structural model will be simulated by I-TASSER (Zhang, BMC Bioinformatics 2008).

 
Online prediction results
 
Once the prediction process is finished, CRHunter will provide a webpage to illustrate the prediction results. As shown in the following figure, the results will be displayed from four perspectives. The first section provides summary information about the query protein and its optimal template. Especially, the predicted catalytic residues are highlighted in red color in the sequence. The second section shows graphical representation of prediction results, in which STRscore, SEQscore, and COMscore denote the prediction scores generated by the structure-based module CRHunter(str), sequence-based module CRHunter(seq), and integrative algorithm CRHunter, respectively. The third section provides three-dimensional visualization of prediction results, in which the putative catalytic residues are highlighted in red sticks. The last section includes the details about the prediction results, including the outputs from our proposed different predictors as suggested in the manuscript. You can also download the results from the hyperlink provided in the first section.