pymol-users

[PyMOL] tertiary structure/protein folding

[Grace C. <go...@le...>]

Hello,
I am trying to model my protein of interest using the builder function in
version 2.3. Is there a way to induce protein folding to properly mimic
tertiary structure, or is secondary structure the highest manipulatable
level of protein order in PyMol?
Thank you,
Grace

Re: [PyMOL] tertiary structure/protein folding

[Tamas H. <bio...@gm...>]

Hi,

Predicting tertiary structure with high accuracy is the holy grail...
I can suggest to perform homology modeling. See Modeller.
If your target is small, you can use molecular dynamics (w replica 
exchange).

Tamas

On 2020. 05. 21. 18:49, Grace Ciabattoni wrote:
> Hello,
> I am trying to model my protein of interest using the builder function 
> in version 2.3. Is there a way to induce protein folding to properly 
> mimic tertiary structure, or is secondary structure the highest 
> manipulatable level of protein order in PyMol?
> Thank you,
> Grace
>
>
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Re: [PyMOL] tertiary structure/protein folding

[KurtYilmaz, N. <Nes...@um...>]

Hi Grace,
You may want to use a protein homology modeling software for more advanced structure building, such as Modeller.
https://salilab.org/modeller/

Nese

________________________________
From: Grace Ciabattoni <go...@le...>
Sent: Thursday, May 21, 2020 12:49 PM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] tertiary structure/protein folding

Hello,
I am trying to model my protein of interest using the builder function in version 2.3. Is there a way to induce protein folding to properly mimic tertiary structure, or is secondary structure the highest manipulatable level of protein order in PyMol?
Thank you,
Grace