Latest News
March 08, 2007
There is a nice
mention
of the Ribosome Builder project in Dr. Ahern's
Best of the Web column in the Mar 1 2007 issue of Genetic Engineering & biotechnology News.
This has motivated me to resume updating the project website, which has been inactive
for a while due to work on other projects.
The first change has been a minor update in the
instructions
for accessing the code via anonymous cvs on the Development page. Stay tuned for further updates.
June 29, 2005
An
article describing the Ribosome Builder has been published in the journal of
Computational Biology and Chemistry:
|
|
| Ribosome Builder: a software project to simulate the ribosome.
| | Comput Biol Chem. 2005 Apr;29(2):163-74.
|
|
The article gives an overview of the software, along with several applications.
Contact William Knight if you are interested in obtaining a preprint of the article.
A whitepaper describing the Ribosome Builder project is also now available, in the form of
a doctoral dissertation by William Knight. This paper presents the theoretical background,
software architecture and several applications of the rbuilder program. The paper is
available for download in the following formats:
January 11, 2005
Version 0.3.4
has been released. This is a regular release of the program to incorporate additions
and changes that have been made in the months following the previous release, 0.3.3.
Significant additions include a schematic simulation of translation elongation. This is a 3D animated
simulation of one complete cycle of elongation on the ribosome, using structural models at atomic
resolution. The simulation can be run by choosing the menu item from the
Script->Other->Demos->Schematic Simulations menu. The simulation incorporates text, graphics,
changing viewpoints, geometrical interpolation of rigid-body structural models and recorded movies of
molecular dynamics trajectories. This type of simulation is expected to becoming increasingly useful in the
future to investigate and communicate models of complex macromolecular systems.
The simulation has been included in the full distribution because it represents an important
demonstration of the capabilities and potential of the main program. However, as a consequence, the file
size of the complete package is rather large, ~25 MB. The size of the core program itself is only around 5
MB. Multiple components have been combined into a single file to simplify the downloading and installation
of the program. However, the strategy for subsequent releases may be to employ more numerous but smaller files.
See the ChangeLog in the
File Release notes
for more details of other additions and changes. Users are encouraged to ask questions
and provide feedback via the Forums page.
September 6, 2004
Version 0.3.3
has been released. This is a regular release of the program to incorporate additions
and changes that have been made in the months following the previous release, 0.3.2.
Significant additions include a game, The Ribosome Builder Game . This is a
little script that requires the player to reassemble fragments of the 16S RNA chain of the small
ribosomal subunit. In addition to demonstrating the challenges of assembling molecules in 3D space,
the process may serve as a means of becoming familiar with the specific shapes and motifs of the
ribosomal RNA structure. The game can be run by choosing the menu item from the
Script->Other->Demos->Games menu.
See the ChangeLog in the
File Release notes for
more details of other additions and changes.
Users are encouraged to ask questions and provide feedback via the
Forums page.
July 2, 2004
Version 0.3.2
has been released. This is an regular release of the program to incorporate the feature additions
and bug fixes that have been done in the two months following the previous release, 0.3.1.
Significant additions include full support of graphics export to POVRAY, file drag-and-drop, a
partially-completed unit test suite of the rbq lua API, updates of the associated html
documentation for the rbq lua API and the high-level lua library, torsion angle frequency report
scripts, feature scripts to select and label inter-subunit bridge residues, and graphical torsion
dials for torsion script objects. See the ChangeLog in the
File Release notes for
full details.
[older news]
| 