Help! Programs for RNA 3D structure???

Francois Major major at
Fri Oct 15 08:26:11 EST 1993

> In article <1993Oct14.210014.13035 at>
> jovinel at it.unimi.csi.imiucca (Luca Jovine) writes: 
>   Dear Netters,
>   I am desperately looking for a program that could generate a
>   3D picture of an RNA molecule (specifically a tRNA), either
>   by energy minimization of input secondary structures (I have
>   heard that a program called StemFile can do this, does anybody
>   Know where to get it or a reference?), or by fitting the 2D data
>   together with known tertiary interactions on a start-up 3D 
>   structure,

Perhaps the program MC-SYM could help you (Major et al. 1991, Science,
253:1255-60).  Primary, secondary and tertiary structural information
is described in an input script.  Then, the program produces a set of
3-D models (in PDB format) that fit the input data.  The program was
used to reproduce the 3-D structure of a tRNA from structural
constraints that were predicted prior to the determination of the
X-ray crystal structure of the tRNA (Major, Gautheret and Cedergren
1993, Proc. Natl. Acad. Sci., in press).

>   based on the data of homologous crystallized molecules.

One of the difficulties of RNA 3-D modeling is the few number of
crystal and NMR structures (compared to proteins).  You can find a
study about the available structures and their use for 3-D modeling in
Gautheret, Major and Cedergren 1993, J. Mol. Biol., 229:1049-1064.

>   If you know anything, references included, please let me know!
>   Thank you in advance...
>					Luca Jovine

To get more information about MC-SYM, send a message to
mcsym-request at
Francois Major                                8600 Rockville Pike
National Center for Biotechnology Information Building 38A, room 8N-805
National Library of Medicine                  Bethesda, MD 20894
National Institutes of Health                 phone: (301)496-2475
                                              fax:   (301)480-9241

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