I have spent a lot of time and patience on the development of an interactive real-time molecular-modeling and -dynamics program called YASARA ("Yet Another Scientific Artificial Reality Application"). The project was my master's thesis at the Institute of Microbiology / University of Graz, Austria and currently contains 60000 lines C- and Assembler-code. With YASARA as some sort of "qualification proof", I am now searching for a PhD position in the area of bioinformatics.

All the details can be found at my homepage: http://www-stud.kfunigraz.ac.at/~kriegere/

Some additional facts about YASARA, just in case you want to read more before activating your browser:

• The main goal was the optimization of the price/performance ratio: YASARA has been developed for Intel/AMD processors, either single PCs or linked clusters of many computers.
• The FTS3D ("Faster Than a Snail" 3D)-engine is aimed at the fluid display of large molecules (>30000 atoms, space fill or wire frame) in true 3D (shutter glasses).
• Molecules can be moved around in three dimensions using an ultrasonic pointer.
• The YASARA force field is based on molecule-trees, statistical analysis of protein structures and off-center point charges.
• A virtual ribosome helps to calculate protein folds.
• NMR: Protein structures can be calculated based on NOESY distance restraints and the YASARA force field.
• Fold prediction: A crude method for bridging the gap between secondary and tertiary structure has been established.
• Automated docking with three degrees of freedom: YASARA searches for the binding site of alpha helices inside the major DNA groove.
• Parallel molecular dynamics with an interactive real-time display, using freely importable force fields (e.g. AMBER). It is possible to pull atoms/molecules around, allowing the interactive modeling of large complexes.

Elmar Krieger