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Frequently Asked Questions

  1. How do I retrieve ConSurf-DB results based on List of PDB id's?

  2. For this exact purpose we added a perl script that retrieves ConSurf-DB results directly from ConSurfDB website according to the input list (see the example bellow). Download and execute the perl script together with your PDB id's list in a separate folder (ConSurfDB files would be downloaded to this folder) Here are additional instructions and info:
    Click here to download the Script - ConSurfDB_list_feature.zip

    Steps:
    - Read the list input file and covert to uppercase.
    - Split and seperate the chains from the PDB id's.
    - Look for the representative pdb ib and chain for each entry
    - Retrieve each chain from the ConSurfDB website

    Notes:
    - the program takes a single command line parameter, all other parameters
    - the working directory for the script is the directory of the given input file. all files are created there.
    - a log file ConSurfDB_list.log is created in the working directory
    - a corrected list file - Corrected_list.dat (with representative chains) is created in the working directory

    Usage:
    ConSurfDB_list_feature.pl input_file
    input_file - List of PDB id's and chains for example - 2DU3 A,B,C,D

    Example of input_file - List of PDB id's with chains:
    1EOV A,B
    1B75 B
    1EFV A
    1ZE1 C,D
    1A1T A,B
    1TUI A
    1QRS B,D
    1NYl A
    1LI7 A