Re: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ?

From: Jiri Sponer <sponer.ncbr.chemi.muni.cz>
Date: Sun, 4 Nov 2007 14:01:02 +0100 (MET)

Although I do not fully understand from your description
what is the exact question, you may find quite
extensive RNA bulge base analysis in this recent study:
http://www.biophysj.org/cgi/rapidpdf/biophysj.107.110056v1
There are some criteria for bulge in/out etc. and I think
also references.

Best wishes

-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
-----------------------------------------------------------



> Dear all,
> I'd like to use PTRAJ to decide whether extra-helical or intra-helical bulge conformation (even the level)
> for ADE16 & ADE17 of the RNA fragment r(5'-GCGUCACACC-3')/r(5'-CGCUGAAGUGG-3') in a 20ns MD simulation by SANDER.
> (The extra-helical for ADE15 & ADE16 structure is like the PDBID: 1PBR)
> Is there any formula (implemented by dealing with several backbone parameters from PTRAJ) or publication on this issue?
> Thank you!
>
>
>
> Best Regards,
> sychen.
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Received on Wed Nov 07 2007 - 06:07:06 PST
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