You got only one match in your sequence search because you ran a search for only one chain.
But because your template and target are HOMOdimer use as alignment file in your .top script this kind of alignment:
>P1;Template
StructureX:::::::
AAAAAAAAAAAAAAA/AAAAAAAAAAAAAAA
>P1;Target
Sequence::::::
BBBBBBBBBBBBBB/BBBBBBBBBBBBBBBB
good luck,
Eric
--------------------------------------------------------
Eric Feyfant, Ph.D.
Department of Biological Chemistry
WYETH Research
85 bolton St.
Cambridge ,MA 02140
tel: (617) 665 8987
fax:(617) 665 8993
email: efeyfant(a)genetics.com
>>> R Senthil Kumar <skumar(a)www.cdfd.org.in> 11/29 7:11 PM >>>
Dear Eric,
Thank you very much for your reply.Eric i will tell my problem clearly.
I am having a protein of 274 amino acids.When i searched for the template
for this protein
it picked up the template which is of homodimer in nature.
i.e, it is having
aaaaaaaaaaaaaa/aaaaaaaaaaaaaaaaa(two chains).My protein is also belong to
the same family of template.In this family homodimer is of active form.
My protein matching with only to the first chain.
If i go ahead with this alignment i will get my peotein in monomeric form.
My question is
1.Whether i can go ahead and get my protein in monomeric form and after
that i can do any trick to convert it into homodimer form-->how to do
this.
2.else in the alignment itself can i do any trick so that i can get
homodimer model of my protein--->how to do this.
If you tell me it will be of very helpful to me.Expecting reply from you.
from,
Senthil kumar.R
R.Senthil Kumar,
Junior Research Fellow(JRF),
c/o Dr.Akash Ranjan,
Computational & Functional Genomics Group,
Centre For DNA Fingerprinting(CDFD),
Hyderabad-500 076
Ph:040-7151344-Extn(Lab:1304)
(Hostel:2300)
E-mail:skumar@www.cdfd.org.in
On Wed, 28 Nov 2001, Eric Feyfant wrote:
> Dear Senthil;
>
> I don't understand something you said:
>
> you have an homodimer to model: seq: AAAAAAAAAAAAAAA/AAAAAAAAAAAA
> You got a template that is an other homodimer so with sequence like: BBBBBBBBBBBB/BBBBBBBBBBBBB (/ separate the 2 chains).
> Now you say that you got a match for only one chain????
>
> if you can align 1 chain you should be able to align the 2nd chain since in the homodimer the 2 chains are identical?
> So the alignment should look like :
>
> AAAAAAAAAAAAAA/AAAAAAAAAAAAAA
> BBBBBBBBBBBBBB/BBBBBBBBBBBBBB
>
> Now if you know the binding site between the 2 chains are different (not only in sequence but also the binding site location) the situation is more complicate and I will suggest you to use biological data and do the docking manually or using docking software like ftdock where you can specify known interaction.
>
> For any further question, I will be happy to help you.
>
> Eric
>
> --------------------------------------------------------
> Eric Feyfant, Ph.D.
> Department of Biological Chemistry
> WYETH Research
> 85 bolton St.
> Cambridge ,MA 02140
>
> tel: (617) 665 8987
> fax:(617) 665 8993
> email: efeyfant(a)genetics.com
>
> >>> R Senthil Kumar <skumar(a)www.cdfd.org.in> 11/28 9:06 PM >>>
>
> Dear modeller users,
>
> I am modelling a protein which is of homodimer in nature and this protein
> matched with the same family protein which is also of homodimer.
>
> But matching with the only one chain(of two chains).So , i got a model in
> a monomer form.How i have to use the modeller to get the replicate of
> other monomer so my model will be of homodimer in nature.Please suggest me
> ideas to overcome this problem.Thanks in advance.Expecting reply from your
> people.
>
> ********************************
> R.Senthil kumar
> Junior Research Fellow(JRF),
> C/O Dr.Akash Ranjan,
> Computational & Functional Genomics(CFG),
> Centre for DNA Fingerprinting & Diagnostics(CDFD),
> ECIL road, Nacharam,
> Hyderabad - 500 076.
> India.
>
> E-mail:skumar@www.cdfd.org.in
> senkumar7(a)yahoo.com
>
> Ph.no:040-7151344-EXTN(1304)--->Lab
> (2300)--->Hostel
>
> ********************************
>
>
