[gmx-users] Membrane protein insertion/orientation methods

[Tsjerk Wassenaar]

Hi Yasser,

InflateGRO and g_membed do not predict the insertion or orientation, but
require the protein to be oriented already. With InflateGRO2, Christian
Kandt also brought out LAMBADA which may help aligning a protein with the
membrane. memembed is also an orientation predictor. However, I usually
just get the protein from the orientations of proteins in membranes (OPM)
database at http://opm.phar.umich.edu/

Cheers,

Tsjerk

On Fri, Aug 21, 2015 at 10:16 AM, Yasser Almeida Hernández <
yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:

> Hi all,
>
> Among the methods available, which one is the best/more rigorous/popular
> for membrane protein insertion/orientation in model bilayers (InflateGRO,
> Memembed, g_membed, etc.)?
>
> Thanks in advance
>
> Yasser
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernandez at chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
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-- 
Tsjerk A. Wassenaar, Ph.D.