AMBER Archive (2009)

Subject: Re: [AMBER] Custom RNA modeling

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Mon Dec 14 2009 - 16:08:07 CST

I think you do not understand complexity of RNA 2D structure
prediction, not speaking about RNA 3D structure prediction,
which is close to impossible task from sequence. Unless
you see clear sequence signatures of some established
RNA motifs with known 3D structures.
So I suggest first to carefullu read literature about RNA 2D predictions.

Regarding simulations, you typically nead good atomic resolution
starting structure as the start, then you possibly can make
some base substitutions. I can hardly imagine using
structure prediction programs as inputs for MD.
We have this review on ACS web page available
Ditzler et al.: Molecular Dynamics and Quantum Mechanics of RNA:
Conformational and Chemical Change We Can Believe In.
Accounts of Chemical Research, in press.
See also for example
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes
studied by molecular dynamics. Biophysical Journal 93, 2007, 3932-3949
how difficult is to converge simulation results of one
sequence starting from four different and conflicting experimental strucures,
one X-ray and three NMR in this case.

Best wishes Jiri

-------------------------------------------------------
Jiri Sponer
Professor of Biochemistry
Head of Department of Structure and Dynamics of Nucleic Acids
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer_at_ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
-----------------------------------------------------------

[ Charset ISO-8859-1 unsupported, converting... ]
> What we are trying to do is to input a nucleotide sequence and predict the
> 3D RNA structure for it. Since it is not an exact science, we want to
> compare the results from different programs. So, for example, we would get
> a prediction from both AMBER and MCSYM and compare the results. After that,
> we would like to do MD simulations on that RNA structure. Hopefully, that
> helps in describing what I am looking for.
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