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.hernan...@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.hernan...@chemie.uni-hamburg.de > office: Grindelallee 117, room 250c > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
