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

[Bozidar Jerkovic <>]

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, "" <> 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  <>
> To: 'R Senthil Kumar' <>,
> 
> CC: 'Bozidar Jerkovic'  <>
> 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: 
> [">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:
> 
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