[gmx-users] ITD-Modelling

[Torsten Stauder]

Hello mailing-list!

Actually I'm about to create a model of a tyrosine-receptor-kinase
(named FLT3 - pdb-code: 1rjb). However, the problem is that I have to
model a mutation of this receptor. A point mutation would be easy to
handle, but in my case the receptor contains a so called "internal
tandem duplication" which is an insert whose length is ~13-30 amino
acids at a specific point. The origin of the inserted sequence is from
the same exon, so the native folding-structure of this sequence within
the wild type is known.

Example (just to illustrate!):

wild type:

XXXXXXXXXXYYYYYYYYYY

mutation
XXXXXXXXXXaaaaaaaaaaaaaaaYYYYYYYYYY    (a = itd)


Any suggestions how to model such a ITD-sequence into a wild type receptor?
I guess this issue is not directly related to gromacs, but maybe you
have some hints anyway, as I didn't find any discussion boards for this.

Thanks so far.