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: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of R Senthil Kumar Sent: Tuesday, February 19, 2002 8:12 PM To: modeller_usage@salilab.org 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:skumar@www.cdfd.org.in