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@genetics.com
>>> R Senthil Kumar skumar@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@genetics.com > > >>> R Senthil Kumar skumar@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@yahoo.com > > Ph.no:040-7151344-EXTN(1304)--->Lab > (2300)--->Hostel > > ******************************** > >