Welcome to the LOGICOIL help page: Information on standard format for input.




The input can be entered in two different formats

  1. As a whole protein sequence:

  2. For cases where you have a whole protein sequence or a coiled-coil sequence with unkown register assignements. Marcoil will be used to detect and assign any coiled-coil region in the input protein sequence and/or assign a register to the coiled-coil sequence. The coiled-coil region predicted by Marcoil will then be parsed through LOGICOIL in order for its oligomeric state to be predicted. (Note: There also exists the possibility that Marcoil does not find any coiled coil region in your protein sequence. In this case, set the Marcoil confidence threshold to a lower value.)

    >[jobname]
    [sequence]

    For example:
    >1EZ3
    VDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKE
    ELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTL
    SRKFVEVMSEYNATQSDYRERCKGRIQ

  3. As a pre-defined coiled coil sequence with assigned register:

  4. For cases where you have a known coiled coil sequence with known register assignements, and wish to find out its oligomeric state. In this case, your coiled coil sequence will be directly parsed through LOGICOIL in order to predict its oligomeric state.

    >[jobname] register [register assignment]
    [sequence]

    For example:
    >1a93 register abcdefgabcdefgabcdefga
    EQKLISEEDLLRKRREQLKHKL