Help! Programs for RNA 3D structure???

Francois Major major at
Fri Oct 15 07:35:14 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,
253:1255-1260).  The input consists of a script in which primary,
secondary and tertiary structural data is described.  The program
produces a set of 3-D models (in PDB format) that fit the input data.
The program has been used to reproduce the three-dimensional structure
of a tRNA from structural constraints that were predicted prior to the
determination of the crystal structure (Major, Gautheret and
Cedergren 1993, PNAS, in press).

> based on the data of homologous crystallized molecules.

An interesting challenge in RNA modeling comes from the fact that very
few crystal or NMR structures are available (compared to proteins).
Find a study of the available structures and their use for 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...

To get more information about MC-SYM and its availability, 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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