SCORER

Standard format for input.



##### Input can be entered in two different formats #####

As a whole protein sequence:



This format can be used in two cases:
  1. If you have a whole protein sequence, and wish to find out whether it contains a coiled-coil.
    In this case, Marcoil will be used to detect and assign any coiled coil region in the input protein sequence. The coiled coil region predicted by Marcoil will then be parsed through SCORER 2.0 in order for its oligomeric state to be predicted.

  2. If you have a coiled coil sequence but do not know the register assignements.
    In this case, Marcoil will be used to assign a register to the coiled coil sequence. The coiled coil sequence is then parsed through SCORER 2.0 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]


An example of a standard input for protein sequences is shown below:

>1EZ3
VDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEKTKE
ELEELMSDIKKTANKVRSKLKSIEQSIEQEEGLNRSSADLRIRKTQHSTL
SRKFVEVMSEYNATQSDYRERCKGRIQ

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



This format can be used in a single case:
  1. If 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 to SCORER 2.0 in order to predict its oligomeric state.

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



An example of a standard input for coiled coil sequences is shown below:

>1a93 register abcdefgabcdefgabcdefga
EQKLISEEDLLRKRREQLKHKL

*Note: Jobname of input is case-insensitive.

University of Bristol