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 QuasarX 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 BioX software) performing this task for you. Use an editor to generate the file (as shown below for BioX) and make sure it is executable (chmod +x RunBioX):
cd $HOME/Desktop/BioX_Linux (if you downloaded the software to there)
java -jar BioX_4.6.4.jar &
· 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 BioX or YetiX for protein modeling? BioX is our most recent software for this purpose and can handle most tasks that YetiX can. In addition, it allows for in situ model building. In YetiX, apolar H atoms (i.e. bound to C atoms) are represented implicitly whereas in BioX a full-atom representation is used. YetiX employs a mixed internal/cartesian mimimizer (which might be superior for interactive docking), whereas BioX 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 BioX and QuasarX 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.