Hello!

Here is what I've tried for my protein's Cterm which did not align with any of my templates:

1- 2D structure prediction using only algorithms with at least 75% overall accuracy as determined monthly by EVA (http://salilab.org/~eva/), and using a consensus of all results as my final prediction 2 - This confirmed that the Cterm domain was probably all alpha since all proteins of known structure in this family of proteins have an all-alpha Cterm 3 - I then used the following script (it's an old .top file - there may be a new example using Python in the Modeller FAQ) for Modeller to set restraints for those last residues that were not aligned against any of the templates:

INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'alignment.ali' SET KNOWNS = 'xxx' 'xxx' 'xxx' SET SEQUENCE = 'xxxxxx' SET ATOM_FILES_DIRECTORY = '/xxx/xxxxxxx/xxxxxx/xxxx/' SET STARTING_MODEL = 1 SET ENDING_MODEL = 20 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '461' '465' RETURN END_SUBROUTINE

-Charlotte Habegger-Polomat

Lucas Bleicher wrote:

>--- Charlotte Habegger-Polomat >chpoloma@rsvs.ulaval.ca a écrit : > > > >>Andy, >>There may be a better answer but depending on the >>length of the gaps >>where structure information is lacking, you could >>use 2D structure >>prediction programs for those regions and then >>impose certain restraints >>on Modeller. For example, the last 10 residues in my >>protein of interest did not have anything to align >>with in the sequences of the 4 templates. >> >> > >That's an interesting approach - I always cut the >terminals of my modeled sequences when I have nothing >that align with it. If it's not asking much, could you >provide an example of how to do this in Modeller? > >Thanks in advance, >Lucas > > > > >___________________________________________________________________________ >Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger >Téléchargez cette version sur http://fr.messenger.yahoo.com > > >