Re: Homologous structure as stating flexible fitting model

From: Zhang Yan (yanzhang_at_moon.ibp.ac.cn)
Date: Wed Nov 06 2019 - 20:39:23 CST

Hi Miro,
What I want to do is flexible fitting a high-resolution structure to a low resolution cryo-electon microscopy density map. And the high resolution structure is a homologous model downloaded from PDB data bank. Which collective variable I need to use?
Thank you very much!
Yan
> 在 2019年11月6日,下午3:27,Miro Astore <miro.astore_at_gmail.com> 写道:
>
> Hi,
>
> What are you trying to do exactly? Are you trying to constrain a different one protein to keep the same tertiary structure as your homologous model?
>
> If so you should be able to use a collective variable. If you're trying to use MDFF, I don't have experience here sorry but I'm sure someone will.
>
> As regards to your sequence question. You will not need to change the sequence, you will have to choose which section of the longer protein corresponds with the shorter one and then you simply NAMD to use the CAs as your reference for your collective variable.
>
> We'll need a bit more detail though.
>
> Best, Miro
>
> On Wed, Nov 6, 2019 at 6:12 PM Zhang Yan <yanzhang_at_moon.ibp.ac.cn <mailto:yanzhang_at_moon.ibp.ac.cn>> wrote:
> Hi all,
> I want to perform flexible fitting using NAMD2, but my starting model is a homologous structure, which the sequence is not the same as my sample. Is it necessary to change the sequence to mine? If so, how can I change the homologous structure’s sequence to mine sequence?
> Their length is different, I don’t how to change it to be the same. Any suggestions or help are appreciated.
> Best
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>
>
>

张艳
Yan Zhang,
Associate Professor,
Institute of Biophysics,
Chinese Academy of Sciences

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