Template Program (Download)

    We have developed a template program, called TargetSRobot, which can be used to automatically access the TargetS web server. TargetSRobot read protein sequences from an input file (query_sequences.txt) and then send the sequences to the TargetS for prediction in turn. The prediction result page of each sequence is an html page and will be saved in the outputs directory.

    TargetSRobot.rb – template program written with Ruby programming language.

    query_sequences.txt – input file which contains protein sequences for prediction.

    outputs – outputs is a directory which contains the result pages (htmls) of the query sequences.

    Each sequence in query_sequences.txt should take the following format:

    >sequenceName  queryConfiguration

    sequence

    Note that queryConfiguration is a 12-digital 0-1 mask code denoting which types of ligands should be considered for prediction by TargetS. The order of 12 types of ligands is as follows:

    Ca²⁺, Zn²⁺, Mg²⁺, Mn²⁺, Fe³⁺, ATP, ADP, AMP, GDP, GTP, DNA, HEME 

    Taking 1xefA as an example, suppose the mask code for prediction is 000001100001 as follows:

    >1xefA  000001100001

DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYI
PENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMS
VEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVN
NPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAARLSTVKNADRII
VMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD

    Then, the TargetS will perform ATP, ADP, and HEME binding sites prediction for 1xefA as the codes for ATP, ADP, and HEME among the mask code are 1s, while the codes for other ligands are 0s.

    Caution 1: considering the computation time, we limited that the maximal number of ligand types for prediction to be 5. In other words, the maximal number of 1s in the 12-digital mask code should not be greater than 5.
    Caution 2: if the mask code takes the form of 000000000000, i.e., none of the ligands was set for prediction, the TargetS will perform prediction by assuming that user choose ‘I don’t know the ligand types’.
    How to run TargetSRobot:
    (1) Unzip the downloaded file TargetSRobot.zip to a directory, e.g. C:\Test.
    (2) Method 1: Enter the directory C:\Test and double click the TargetSRobot.rb file.
    (3) Method 2: Open a DOS window and enter the directory C:\Test, then input 'ruby TargetSRobot.rb' on the command line as follows:
           C:\Test>ruby TargetSRobot.rb
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