Hello,
I´m having a problem that I would like to
know if someone could help me.
I want to do a 3D structure based alignment
of my protein with another one. The problem is that my protein has 2 domains,
and the structure that I want to superimpose just have one. I can do the
structure superimposition by hand, but I´m not being able to do the sequence alignment
based on the 3D structure, because the program that I´m using (SSM) starts to
superimpose the sequence of my second domain in the beginning of the sequence
of my reference model (exactly the same thing that it does with the sequence of
the first domain).
Do you know if there is any program where I
can do this.
Thanks in advance,
Tânia Oliveira, PhD Student
Membrane Protein Crystallography and
Microbial Biochemistry Laboratory - ITQB-UNL