Subject: YASARA

From: <[email-masked]>
Date: Thu, 16 Sep 1999 19:55:56 +0200

From: "Elmar" <[email-masked]>

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:

[email-masked]

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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