From chemistry-request@server.ccl.net Thu Sep 16 17:13:52 1999 Received: from sparrow.prod.itd.earthlink.net (sparrow-e.prod.itd.earthlink.net [207.217.118.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05729 for ; Thu, 16 Sep 1999 17:13:50 -0400 Received: from lrz.de (1Cust251.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.251]) by sparrow.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id OAA04685; Thu, 16 Sep 1999 14:07:25 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id OAA17315; Thu, 16 Sep 1999 14:04:48 -0700 Resent-From: Eugene Leitl Resent-Message-ID: <14305.23407.967310.117084@lrz.de> Resent-Date: Thu, 16 Sep 1999 14:04:47 -0700 (PDT) Resent-To: , , , , Message-Id: <001a01xxxbf006d$42126400$5f21328f@sgi-onyx-1> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Precedence: bulk From: To: Subject: YASARA Date: Thu, 16 Sep 1999 19:55:56 +0200 From: "Elmar" 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@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 *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/forum.html ***