YASARA

 From: "Elmar" <elmar.krieger (- at -) kfunigraz.ac.at>
 Dear PDB Users,
 during the past 18 months, 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
 Comments that are too specific for the public can be directed to:
 elmar.krieger (- at -) kfunigraz.ac.at
 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.
 Thanks a lot for your attention and transmission bandwidth,
 best greetings from Austria,
     Elmar Krieger
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