Table of contents
   1. Submit Job
   2. Input File
   3. Output File
   4. Error Masseges
     Submit Job
     
     
        AnkPlex aims to easily and efficiently provide near-nartive complexes of ankyrin-protein by ranking LGS score based on scores calculated from ZDOCK program. The user needs to do 2 steps.
        Step 1: Docking the ankyrin and its target in ZDOCK program. Several docking complexes with their scoring feature are generated.
        Step 2: Uploading the docking ID together with its scoring. The scoring features of docking complexes are combined to get LGS score. The near-nartive ankyrin-protein complex (es) are found in 10 top LGS score.

Step 1: Docking the ankyrin and its target in ZDOCK program

There are 2 protocols for obtaining docking poses and their scores.
(1) ZDOCK protocol
        To generate a huge number of near-nartive complexes of ankyrin-protein, the parameters in this protocol shoud define as below suggestion.
             - Defining binding residue of ankyrin:   positions 2, 3, 5, 13, 14, and 33
             - ZRank:   True (rank docking complexes by Zrank score)
             - Report Score Components of ZRank:   True
             - RMSD Cutoff of the Clustering:   6
             - Interface Cutoff of the Clustering: 9
             - Use Electrostatic and Desolvation Energy: True
        The energy scores of this protocol are used for calculating the LGS score consist of ZDock, ZrankElec, Zrank score, ZrankSolv, and ZrankVdw

(2) RDOCK protocol
        All generated docking complexes from ZDOCK protocols are recalculated the energy function using defult parameter. The scores of E_elec1, E_vdw1, E_elec2, E_vdw2, E_sol, and E_RDock are used for calculating the LGS score.

     
Step 2: Uploading the docking ID together with its scores.

        When the user arrives at the AnkPlex page, the user can see the section of loading file that is put the docking poses and their scores. Please follow the below substeps to obtain the prediction.
(2.1) Click the "click here" button to dowload the template file (Table 1).
(2.2) Put the docking name and its score in dowloaded file and save file (Table 2).
(2.3) Upload the template file that already be put the docking data.
(2.4) Click "submit" button to send the input file.
(2.5) Wait for executing until the progress shows 100%.
(2.6)
Look at the "RESPONSE MESSAGE" in the output box. If the prediction is successful, the "RUNNING SUCCESSFULL!!" is shown together with output file that the user can get by click on "Click here" button. If the running is fail, the ERROR MESSAGE is shown to guide the user how to solve it.
     
   
 
Figure 1. The AnkPlex page showing the uploading section.
 
   
  Figure 2. The result after finishing the prediction on AnkPlex page.  
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     Input File
     

 

        The fields in AnkPlex_template file are the names of docking pose and the 11 scoring features are provided from ZDOCK program. The Table 1 is the example of the original AnkPlex_template file. In this file, the first row called heading describes the names of docking pose and scoring features that should be put value in. Please do not delete or edit anything on the heading row. The values of scoring and also docking name should start from the second row as the example showed in Table 2.
 
Table 1 Example of template file
Table 2 Example of input file

Scoring features from ZDOCK program

  • ZDock is the shape complementarity score (and also includes electrostatic and desolvation energy). 
  • ZRankElec is the long range electrostatics energy and only full charged side-chain are used to calculate.
  • ZRank score is a linear combination of van der Waals, electrostatics, and desolvation energy. 
  • ZRankSolv is the desolvation term based on Pairwise Atomic Contact Energy (ACE).
  • ZRankVdw is the van der Waals and short range electrostatics energy, distance between atom pair is < 5.0 Å.
  • E_vdw1 is van der Waals energy after first minimization with ionic residues in neutral state. 
  • E_elec1 is electrostatic energy after first minimization with ionic residues in neutral state.
  • E_vdw2 is van der Waals energy after second minimization with ionic residue in charged state.
  • E_elec2 is electrostatic energy after second minimization with ionic residues in charged state.
  • E_sol is desolvation energy based on the Atomic Contact Energy (ACE).
  • E_RDock scoreis a summation of E_sol and (0.9 x E_elec2). 
     
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     Output File
     
     
        When the calculation process is successful, the output file can be downloaded on the user's screen. The output file is provided in AnkPlex_output.csv file. The two extra columns named Rank and LGS are added before the ID column. Only the docking poses that the LGS is more than 1 are shown and ranked. The near-nartive ankyrin-protein complex (es) can be found in 10 top-ranking LGS.
     
Table 3 Example of output file
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     Error Masseges
     

1. file exeed maximum
    Cause: file size exeeds 2 Mb
    Solve: spliting your file to > 2 files  

2. incomplete file upload
    Cause: the uploaded file was only partially uploaded
    Solve: re-upload again  

3. some error occured during upload
    Cause: cannot define the cause of uploading error
    Solve: re-upload again  

4. file type mistmatch
    Cause: the uploading file is not csv file
    Solve: please change your file type to .csv file  

5. wrong headers
    Cause: the program does not familiar with headers in your input file
    Solve: please download the template here and put your data in this file  

6. no numeric value
    Cause: no data added
    Solve: add your data in file

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