DeepView / Swiss-PdbViewer ========================== http://spdbv.vital-it.ch/ http://www.expasy.

org/spdbv/ ------------------------------------------------------------DESCRIPTION =========== Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain than s to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly lin ed to Swiss-Model, an automated homology modelling server accessible from ExPASy Wor ing with these two programs greatly reduces the amount of wor necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedbac of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain pac ing. NOTE for Win NT: ---------------SPDBV is writing temporary files while running. Please ma e sure, that the installation directory (e.g. C:\spdbv) and all subdirectories have the correct Read/Write permissions for all users wor ing with this installation. HISTORY ======= I started wor ing on Swiss-PdbViewer in 1995 to visualize at home comparative modeling results of one of the enzymes I cloned during my PhD (soybean malate dehydrogenase). The first version was an adaptation of a software I wrote to help a friend of mine produce stereograms during the big "Magic Eye" wave. At that time it was a Mac-only 68K software and had even some assembly code to speed-up display and rendering. Later I joined Manuel Peitsch's group at the Glaxo Institute for Molecular Biology and started to adapt the software to run on Windows NT and serve as a GUI for SWISSMODEL. Later, Alexandre Diemand and Torsten Schwede both contributed to the development: Alexandre ported the GUI to SGI translated Quic Draw3D calls to openGL and contributed to the development of the scripting language. Torsten implemented electrostatic computation and hardware stereo support for the PC version. He also improved the SWISSMODEL server interface and the bac end server allowing to blast and retrieve sequences and structures from the Swiss-PdbViewer interface and he is now in charge of the SWISSMODEL server http://swissmodel.expasy.org//SWISS-MODEL.html I also wish to ac nowledge Wilfred van Gunsteren for the GROMOS96

force field parameters and Barry Honig for the grasp file format, and last but not least, the numerous users who provided feedbac , suggestions, and bug reports. In particular Holger Scheib, David Mathog, Eric Martz, Joe Krahn, Simon Andrews, Mi e Word and Gale Rohdes, who, besides performing ext ensive beta testing since version 0.98 made a wonderful tutorial http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/index.html and also maintains a discussion list. http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/text/DiscuSPV.html Have fun! Nicolas