This page contains links to software programs and tools that can be used in conjunction with
the main course material. All of the software listed is free and open source. Many but not
all programs are multi-platform (GNU/Linux, Windows, Mac).
Games, Demos and Simulations
| AA-Tetris
| Tetris-like game for learning about amino acids
| | Evolution Demo
| Simple demonstration of the principles of evolution
|
2D Structure Drawing
| XDrawChem
| Simple 2D molecular structure drawing program
|
3D Structure Visualization, Modeling and Simulation
| RasMol
| Simple 3D visualization program
| | Jmol
| Good 3D visualization program
| | PyMOL
| Powerful 3D visualization program
| | Ribosome Builder
| Modeling, simulation and visualization program for macromolecular systems
|
AA-Tetris
AA-Tetris is a tetris-like game that can be used to learn the names,
abbreviations and symbols for the side chains of the 20 biological amino acids.
The AA-Tetris game is available here.
Evolution Demo
The 'evo' program is a simple graphical demonstration of evolutionary processes.
The 'evo' demo is available here.
XDrawChem
XDrawChem is a simple 2D molecular structure drawing program.
| GNU/Linux | Windows | Macintosh |
RasMol
RasMol is a fairly small and simple program for viewing 3D molecular models. A
recent version of RasMol for various platforms is available
here.
| GNU/Linux | Windows | Macintosh |
Jmol
Jmol is another good program for viewing 3D molecular models (requires Java). It is
being actively developed (unlike RasMol) and runs both as a standalone application and as an
applet in a web browser.
It is available
here.
| GNU/Linux | Windows | Macintosh |
PyMOL
PyMOL is a larger and more sophisticated molecular visualization program. It is
available at the PyMOL homepage.
| GNU/Linux | Windows | Macintosh |
Ribosome Builder
The Ribosome Builder is a software project for simulation and visualization of
large molecular models and macromolecular systems. The complete version is available
at the
Ribosome Builder homepage.
The above program is rather large because of the built-in demonstrations of
ribosome structure and function. A smaller, stripped-down version is also
provided below. This smaller version can be used for just viewing the
molecular visualization and demonstrations that are created for the BIOC380
course.
Ribosome Builder Lite (3.9 MB)
As additional demo files are created for this version, they will be announced in class and made available
in the 'Games, Demos and Simulations' section above.
|
