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Thanks for everyone who concerns. Here is a simple
summary:
1.get pdb from PDB
2. DNA four-way junctions bound to proteins: in the PDB
site (or in MSD at EBI:
http://www.ebi.ac.uk/msd-srv/msdlite/index.html
3.NAMOT should be able to build any kind of DNA junction.
See examples in http://namot.lanl.gov/
4.you may prefer a "flat" four-way junction, as found in
complex with proteins like in PDB 1c7y (you need to build
some symmetry-related molecules to see the flatten
four-way junction, which in this case is not continuous)
5.learn more about the four way junction: a series of
papers by David M.J. Lilley on junction conformation
(going back to late 1980s)
6.Refer to the supplemental material from Proc. Natl.
Acad. Sci. USA. 2005 May 17;102(20):7157-62 for a survey
of a few published junctions. 7.There are several simple
methods to apply translation and rotation matrices to one
or both of the duplex junction arms if you want to
increase the central cavity size.
Here I am very appreciate for your kindness.
On Wed, 23 Nov 2005 12:50:55 -0800
Jie Li <[EMAIL PROTECTED]> wrote:
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Hi, everyone,
I had no experience on DNA modeling. Now I have to
build a DNA four- way junction. I hope the space in the
middle of junction can big enough. But I cant find a
structure with such junctions.
Does anyone have some opinions or suggestions.
I will be very appreciated.
Lily
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