oped for the generation of models of RNA and protein 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 the Primary Sequence and
the Secondary Structure of the molecule. For the creation of these structu-
res, Version 2.0 PC of ERNA-3D uses the integrated Secondary Structure
Editor, called "ERNA-2D". We assume, that ERNA-2D is the most flexible
and easy to use Secondary Structure Editor world-wide, because all created
parts can directly be moved with the mouse pointer and single strands can
be bent on the screen like a rope.
Whole domains of a molecule can be selected by a frame, which is freely be
drawn by the user. After that, the framed regions of the 2D map of the mole-
cule can be moved with all its contents by using the mouse pointer.
The most important feature of ERNA-2D is its ability to translate the just edi-
ted Secondary Structure directly into the three-dimensional counterpart of
the molecule, which then can be manipulated by the 3D-functions of ERNA-
3D. For this, ERNA-2D translates the individual residues into spatial atomic
coordinates and builts up helical structures and flexible single strands, which
will be bent into forms of Hairpin Loops, Bulges, and Interhelical Loops.
The difference between ERNA-3D and conventional Molecular Modeling Sys-
tems lies in its ability to manipulate parts of the molecule in a dynamic and
realistic manner. Single strands, which are generated as full atomic represen-
tation, can be pulled with a three-dimensional cursor (controlled by the nor-
mal computer mouse) and can be brought into a plausible configuration. For
this purpose a special Chain Translation Algorithm was developed, which si-
mulates the molecular mechanics and performs rotations of molecular groups
about single bonds in the backbone chain of the molecule in real time. This
causes 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 also
the connecting single strands are dynamically be pulled, so that they remain
attached. In contrast to many other commercial programmes the relative loca-
tions 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 mo-
dified model(s) and all user interactions can be viewed in three dimensions on
the computer display with the help of Shutter Glasses or other 3D-technics.
- ERNA-3D has been developed at the Max-Planck-Institute for Molecular
Genetics in
Berlin in the laboratoy of Dr. Richard Brimacombe (AG Ribosomes) and has further
been developed by the company PENTAFOLIUM-SOFT.
- ERNA-3D represents more than 14 years of solo work by the
author.
- All functions were implemented in the computer language "C" and
"C++" using OpenGL(Tm).
- The source codes amounts to more than 280.000 programing lines.
- After a comprehensive porting work, ERNA-3D now runs on personal
computers with
Microsoft(Tm) Windows(Tm) operating systems.
- ERNA-3D has already been successfully used to model the ribosomal
RNA
molecules, and to fit them to corresponding electron density contours.
- Many research groups around the world are already using the ERNA-3D software.