** MODELLER SUPPORT ** RE: Hai modeller people!!!!!!!!

["Bozidar Jerkovic" <>]

Hi,

There is probably not much that you can do to get a model of 3D
structure for that sequence segment, although ab initio modeling with
some of the best methods has some chance of giving you a roughly correct
fold since this is a small domain of a larger protein, I presume. For ab
initio methods, check out the 2000 Progress review by David Baker in
Nature.

What kinds of template search did you tried? Don't rely only of
MODELLER's SEQUENCE_SEARCH. Check out other methods at our web site:
http://salilab.org/bioinformatics_resources.shtml

Thanks,
Bozidar


***********************************************
-----Original Message-----
From: 
[">mailto:] On Behalf Of R
Senthil Kumar
Sent: Tuesday, February 19, 2002 8:12 PM
To: 
Subject: Hai modeller people!!!!!!!!



Dear modellers,

  I am having a doubt in homology modelling.Please help me to overcome
this problem.

I am having a template/target alignment file like this:

>P1;xxx (template alignment)
-------------------------EPTIHKLAGCTA and go on.
>P1;xxx(taget sequence to be modelled)
MTGCATDAERAEPTIGCTAADEGRAEPTIHKLAGCTA and go on.

My question is how to model the region in target sequence that doesn't
have any corresponding coordinates to get from template
sequence.(reference structure).

Kindly suggust me solution to overcome to this problem.Thanks in
advance.

                                         Yours sincerely,
                                            Senthil kumar.R
  
     R.Senthil Kumar,
     Junior Research Fellow(JRF),
     c/o Dr.Akash Ranjan,
     Computational & Functional Genomics Group,
     Centre For DNA Fingerprinting & Diagnostics (CDFD),
     Hyderabad-500 076.
     
     Ph:040-7151344-Extn(Lab:1304)
                        (Hostel:2300)
     E-mail: