[gmx-users] Membrane protein insertion/orientation methods

[Catarina A. Carvalheda dos Santos]

Hi there,

Lambada + InflateGRO2 is a good combination.

As for which method is the best one is difficult to say. If you read the
articles you will have a nice idea of the pros and cons of each method and
then you can decide by yourself. The only thing I can say is that after
reading them all I went for the aforementioned combination ;)

Cheers,
On 21 Aug 2015 10:08, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:

> 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.
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