Thank you very much Sir for the information.
On Tue, Jan 19, 2021 at 3:10 PM Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> We usually use NAB to create the extension in the needed conformation
> adding 1-2 bases (base pairs) common between the extensions and the
> structure. Then, using VMD we superimpose the extensions on the
> structure using the common part. Then, again in VMD we process the
> superimposed structures (delete overlapping bases and so on). Care is
> needed in deciding what to keep/remove depending on the features of your
> structure. If your structure is a protein-bound DNA it may be deformed
> and then you'd like to keep as much as possible from the original
> structure. Same is valid if your structure has a particular conformation
> you are interested in .... We usually do a minimization/equilibration in
> which the extensions are allowed to move while the structure not (not
> sure this is really needed always)
>
> Now, if your DNA is B-DNA, this procedure works quite easily . However,
> if you have a special DNA structure, you need to get some experience
> with NAB to build exactly the type of structure you need. Especially the
> overlapping parts between extensions and structure you probably want to
> have them in a conformation that is the same as in the structure
>
> Best,
> Vlad
>
>
>
> On 19/01/2021 04:57, Airy Sanjeev wrote:
> > I have a protein that is bound to DNA, now I need to extend the DNA
> > structure at both ends. Kindly guide me how to extend the DNA using any
> > software.
> >
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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--
with best regards,
Airy Sanjeev, PhD
Post Doctoral Fellow
Indian Institute of Technology Guwahati, Guwahati
Assam-781039, India
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Received on Tue Jan 19 2021 - 02:30:02 PST
