Hi,

Yes, that's a good idea. You can also try to use THREADER. For more resources and information please visit: http://salilab.org/bioinformatics_resources.shtml

Can you please post all replies and questions directly on the list.

Thanks, Bozidar

On 20/2/02 1:06 PM, "skumar@www.cdfd.org.in" skumar@www.cdfd.org.in wrote:

> > Dear Bozidar, > > Thank you very much for your reply. I have one idea kindly suggest me whether > it is worth of doing it?. > > The part of the target sequence which has insertions in the alignment when > compared to the template structure can we take out that region along with > some anchor residues and search it against fold recognition servers such > as FUGUE server and get the possible template structure against that region > and include that template in the ali file. > > Kindly suggest me your suggestions regarding this.Thank you very much in > advance. > > Yours sincerely, > Senthil kumar.R > > ---------REPLY TO------------- > Date:Tue Feb 19 18:07:14 GMT+00:00 2002 > FROM: Bozidar Jerkovic bozidar@oboe.rockefeller.edu > To: 'R Senthil Kumar' skumar@www.cdfd.org.in, > modeller_usage@salilab.org > CC: 'Bozidar Jerkovic' bjerkovic@mail.wesleyan.edu > Subject: ** MODELLER SUPPORT ** RE: Hai modeller people!!!!!!!! > > 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 > > > > > > > > > > > > > > > > > > > > > > - > > >