Re: [modeller_usage] Question about huge gaps

[flavio seixas <>]

Hi,

Allow me add one more option in this case.
You can use a web server that make secondary structure predictions from sequence, e.g. PsiPred (http://bioinf.cs.ucl.ac.uk/psipred/) and use the result to impose any restrictions in the protein modelling, such as alpha helices or beta-sheet.

Regards,

-------------------------------------
Flavio Augusto Vicente Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br


--- On Thu, 5/30/13, Modeller Caretaker <> wrote:

> From: Modeller Caretaker <>
> Subject: Re: [modeller_usage] Question about huge gaps
> To: "Daron Standley" <>
> Cc: 
> Date: Thursday, May 30, 2013, 7:35 PM
> On 05/30/2013 02:31 AM, Daron
> Standley wrote:
> > Although I'm not a very regular user of modeller, I
> believe it is well
> > known that long gaps, especially terminal gaps, look
> strange when
> > modeled using default options.
> 
> Sure. Typically, we just remove those regions and don't
> model them. Any modeling of these regions is just going to
> be fantasy anyway.
> 
> > "if distance of residue x from center is greater than
> some huge value
> > (2-3x the predicted Rg, based on sequence length), add
> a bias to the
> > potential for x toward the center of the protein"
> 
> The easiest way to do that would be to add an upper bound
> distance restraint between each C alpha and the center of
> gravity of the protein. An example is at
> http://salilab.org/modeller/9.11/manual/node105.html
> 
>     Ben Webb, Modeller Caretaker
> --  
>            http://www.salilab.org/modeller/
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