Software

FAQ

· Who is entitled to download the Biographics software? Everybody.

· For what purposes may the Biographics software not be used? Its use towards the development of compounds associated with biological or chemical warfare is not permitted.

· Where are results obtained with the software published? The pertinent publications are listed in the individual program areas (visible in the panel at the right).

· Can I obtain any support for the Biographics software? Sorry, no.

· What are the system requirements for running the Biographics software? The Biographics software is available for Macintosh, Linux and Windows operating systems and require Java 6 (a.k.a. Java 1.6 or Java SE 6) or higher.

· Does the Biographics software run on 32-bit Linux operating systems? Yes, except Quasar^X where the batch programs (Quasar_IndFit and Quasar_ModBld) were compiled on a 64-bit operating system.

· Running Quasar under Linux/CENTOS: When executing Quasar_IndFit or Quasar_ModBld, the following error may occur: "/lib64/libc.so.6: version GLIBC_2.7 not found". Upgrade to the newest version of CENTOS (6.2) or install UBUNTU 10.4 or higher. Both versions work fine.

· How has the Biographics software to be installed? After download, uncompress the corresponding zip (*.tgz) file. It will generate and populate a corresponding folder including executables, libraries and (if applicable) a demonstration example. Download the documentation and the place it in the very folder. After installation of the jogl libraries (cf. README file), double-click the software icon to launch it or start the program from a shell (see instructions in the README file for Macintosh or below for Linux).

· Upon double-clicking its icon, the program doesn't start up. Most likely, you have installed a version of Java lower than version 6 (a.k.a. Java 1.6 or Java SE 6).

· The program starts up but no molecule can be displayed. Most likely, there are some jogl libraries installed in /Library/Java/Extensions (Mac OS X; corresponding locations under Linux or Windows have a different path). Our software provides those libaries directly and refers to them via a $CLASS_PATH. Therefore, no other libraries may be installed system wide. You can either remove (rename) them in the general location or edit our *.jar files to point to the general location — if that refers to jogl 2.0 (experts only).

· Can I launch the software under Linux (e.g. Ubuntu) by simply double-clicking its icon? This depends on your local installation and settings. You can, however, create a small script (e.g. "RunBioX" for the Bio^X software) performing this task for you. Use an editor to generate the file (as shown below for Bio^X) and make sure it is executable (chmod +x RunBioX):

#!/bin/bash
cd $HOME/Desktop/BioX_Linux (if you downloaded the software to there)
java -jar BioX_4.6.4.jar &

The command files for the Yeti^X, Quasar^X and Momo^X software can be generated accordingly.

· I cannot launch the Quasar batch executables (Quasar_IndFit and Quasar_ModBld) via the provided shell scripts (Run_Quasar_IndFit and Run_Quasar_ModBld) under Mac OS X 10.8.5 or newer. Although all software and shell scripts are signed, the signature cannot be preserved upon copying a script through a program (QuasarX) from one location (QuasarXLibrary) to another (your working directory). Therefore, either copy the script files manually (from the QusarXLibrary folder to your working directory) or launch/use a shell, "cd" to the working directory (hosting your very project) and launch the executables the "normal" way: "./Quasar_IndFit_600 &" and "./Quasar_ModBld_602 &", respectively. The classic executables (with the ".x" ending) are located in the folder QuasarXLibrary. The results, of course, are identical.

· Should I use Bio^X or Yeti^X for protein modeling? Bio^X is our most recent software for this purpose and can handle most tasks that Yeti^X can. In addition, it allows for in situ model building. In Yeti^X, apolar H atoms (i.e. bound to C atoms) are represented implicitly whereas in Bio^X a full-atom representation is used. Yeti^X employs a mixed internal/cartesian mimimizer (which might be superior for interactive docking), whereas Bio^X uses a pure cartesian minimizer (which converges better).

· What is special about the Yeti force field? It is directional and allows for state-of-the-art treatment of hydrogen bonds (distance, linearity, directionality) and metal centers (dynamic ligand–metal charge transfer, symmetry, directionality, LSFE). This force field is used in Bio^X and Quasar^X as well. The latter also includes a term for ligand–protein polarization.

· What does 6D-QSAR (software Quasar) stand for? The fourth dimension in multi-dimensional QSAR (mQSAR) allows for the simultaneous consideration of different orientations, conformations, protonation states, tautomers and stereoisomers (→ 4D-QSAR). The fifth dimension refers to the consideration of different induced-fit scenarios (→ 5D-QSAR). The sixth dimension allows for the implicit or explit simulation of different solvation models (→ 6D-QSAR).

· Can I obtain a free copy of the VirtualToxLab™ for stand-alone use? No, the VirtualToxLab™ runs as a client–server application on our Unix cluster. Non-profit and governmental organizations may apply for a free license (OpenVirtualToxLab) to the technology. On-site installations are exclusively available for industrial customers. Details are given here.