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General information about ERNA-3D:

ERNA-3D is a Molecular Modeling System, which was specially developed

for generating models of small or large RNA molecules. The programme

can also be applied to proteins and other molecules.

Using ERNA-3D it is very simple to build up an array of RNA double helices

containing complex structures such as internal loops, bulges and hairpin loops.

All that is needed for this construction is a very simple structure definition

data file, which contains the information relating to the primary sequence and

secondary structure of the molecule. The individual residues are defined by

capital letters, which the programme translates into spatial atomic coordi-

nates and then builds up the helical structures. Now, Version 2.0 of ERNA-3D

also uses an integrated Secondary Structure Editor "ERNA-2D" which allows

the creation of atomic structures directly out of an edited secondary structure

map.

The difference between ERNA-3D and conventional Molecular Modeling

Systems lies in its ability to manipulate parts of the molecule in a dynamic and

realistic manner. Single strands can be pulled with the mouse and brought into

a plausible configuration. For this purpose a special Chain Translation

Algorithm was developed, which simulates the rotations of molecular groups

about single bonds in the backbone chain of the molecule in real time. This

conveys the impression that one is dealing with a "realistic" molecule. Helices

and parts of the molecule previously defined as constituting a unit (cluster)

can be clicked onto, and then translated or rotated; during this process the

connecting single strands are dynamically pulled as well so that they remain

attached. In contrast to many other commercial programmes the relative

locations of different molecules within a single model can be readily altered.

All the atomic models can be stored in PDB files and then re-loaded. The

modified model(s) and all user interactions can be viewed in three dimensions

on the computer display with the help of Shutter Glasses (obligatory for 3D

viewing).

ERNA-3D at a glance:

* ERNA-3D was developed at the Max-Planck-Institut für Molekulare
Genetik in Berlin in the laboratoy of Dr. Richard Brimacombe
(AG Ribosomen).

* ERNA-3D represents more than 12 years of solo work by the author.

* All functions were implemented in the computer language "C".

* The source codes amount to more than 272.000 programme lines.

* ERNA-3D runs on any current Silicon Graphics computer (under IRIX 6.x).

* The only supplementary hardware needed is a set of Shutter Glasses with an
IR-emitter.

* ERNA-3D has already been successfully used to model the ribosomal RNA
molecules, and to fit them to corresponding electron density contours.

* ERNA-3D is already be used by many research groups around the world.