[gmx-users] PROTEIN FOLDING

[João Henriques]

Depends. If you're interested in local folding and there are SS motifs in
the region you're interested, then yes. If not, no. In terms of overall
folding of the entire protein, yes it surely can be an important analysis.

J

On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysics17 at gmail.com> wrote:

> Thank you Joao and Aman.
>
> I have noted the points you have suggested.
>
> Do you think analyzing DSSP would help?
>
> Thanks,
> Neha
>
> On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
> joao.m.a.henriques at gmail.com> wrote:
>
> > "You can use various supporting tools from R language to debug your
> > trajectory but most third party software support NAMD and charmm format.
> > You can use VMD to convert the trajectory to dcd and use R language based
> > packages to read your trajectory"
> >
> > What? How is this useful or helpful? At most it confuses the OP even
> more.
> >
> > Also, the clustering analysis is unlikely to be what you want or need at
> > this stage. Why overcomplicate? One of the simplest ways to check that
> > there are conformational changes on a given set of atoms is by doing a
> RMSD
> > analysis using the folded structure as the reference. The RMSD is
> somewhat
> > degenerate, but should suffice for this purpose. You can use an index
> file
> > to restrict the RMSD analysis to a particular subset of your system (the
> > docking site, for example).
> >
> > You could look at the radius of gyration as well, Rg, as Aman Deep also
> > suggests. This can either be calculated on a subset of atoms or on the
> > entire protein. The latter could potentially be used to compare with the
> > experimental reference obtained by SAXS, for example. Or you could
> > calculate the SAXS curve and get a better understanding of size and shape
> > differences between your protein and the reference, but that's more
> > advanced stuff.
> >
> > J
> >
> > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Also you must know, a lot analysis are available over the entire manual
> > of
> > > Gromacs where all cannot be performed. Gromacs always provide you all
> > > necessary analysis but to choose which one is always your choice that
> > suits
> > > your simulation purpose.
> > >
> > >
> > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysics17 at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > >
> > > > Thank you for your prompt reply.
> > > >
> > > > By clustering analysis, are you talking about gmx cluster command?
> > > >
> > > > "over particular PC sub space"
> > > >
> > > > Could you please elaborate a bit?
> > > >
> > > > Thanks a lot once again.
> > > >
> > > > Thanks,
> > > > Neha
> > > >
> > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <
> drrahulsuresh at gmail.com
> > >
> > > > wrote:
> > > >
> > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <
> nehaphysics17 at gmail.com
> > >
> > > > > wrote:
> > > > >
> > > > > > Hi gromacs users,
> > > > > >
> > > > > > After MD simulation of protein-ligand complex for 5ns, can we
> view
> > > > > protein
> > > > > > folding?
> > > > > >
> > > > > > How to do it?
> > > > > >
> > > > > > I want to ascertain if there is any conformation change in
> protein
> > > > where
> > > > > > the ligand binds. Is it possible?
> > > > > >
> > > > > > We observe hydrogen bonds through molecular docking. Hence, I
> want
> > to
> > > > > make
> > > > > > observation through MD simulation which is not obtained through
> > > > docking.
> > > > >
> > > > >
> > > > > You can perform Clustering analysis over particular PC sub space to
> > > > measure
> > > > > the structural changes.
> > > > >
> > > > > >
> > > > > >
> > > > > > Can someone help me regarding this?
> > > > > >
> > > > > > Thank you very much in advance.
> > > > > >
> > > > > > Thanks,
> > > > > > Neha
> > > > > > --
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> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
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> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
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