FAQ
Q: What is the CSV format?
A: CSV stands for Comma Separated Values. The first column has entries to denoted different classes and different families are separated by entries in the second column. The family members are in the third column.
| Column | Contains | Possible Values |
| 1 | Entries denoting the protein class that follow | EC number |
| 2 | Entries denoting protein families | "Family. Representative Entry is:" |
| 3 | Protein ID | 4 character PDB ID, uppercase |
| 4 | Ligand Name | Space separated list of HET group names |
| 5 | Ligand Validity* | "valid","invalid" |
| 6 | Affinity Measure | "IC50", "Kd", "Ka", "Ki" |
| 7 | = | "=" |
| 8 | Affinity Value | numeric value |
| 9 | Affinity Unit | "M", "mM", "uM", "nM", "pM", "fM", "M^-1" |
| 10 | SMILES string | SMILES string line noation |
*For definition of valid and invalid please see reference publication.
Q: What is the Eolus Viewer?
A: The Eolus Viewer is a Java(TM) based program developed by Metamatics, LLC (now Torrey Path,LLC ) which allows you to view the protein-ligand cavity for a given crystal structure in MOAD.
Q: How do I get the Eolus Viewer to work?
A: The viewer is Java based and uses Webstart to run a Java Servlet. Thus, you need to have a working Java environment on your computer. Webstart is now distributed as an integral part of Java. The following table is provided to detect if you have Java installed on your machine.
| Java Detection Test | Where to go to Install | |
| 1) Java 1.4+ |
|
Java |
| 2) Java3D |
Click to Test (Points to site outside of Binding MOAD. You should see a rotating cube) |
Java
3D - multiple OS types and versions |
Q: What about Web Start?
A: Because Web Start is distributed as an integral part of the Java JRE, it should be a straight forward installation, and should automatically register Web Start with the Browser of your choice. Web Start is under the JRE directory, where you installed Java (look for a file called "javaws.exe"). Also see Sun's Installation notes.
Q: How do I install the Java Plugin in Linux?
A: You need to install the Java plugin for your browser. Essentially, you need to create a soft link from the plugin in the Java directory, to a directory in you Mozilla folder installation. Some installations of Mozilla(aka Firefox) do not create a "plugins" directory under your .mozilla directory, but a simple "mkdir .plugins" should satisfy that. Please see: Mozilla FAQ
Q: Which do I install, Java JRE or Java SDK?
A: If you just want to run Java software (such as the Eolus viewer), then you just need the Java Runtime Environment (JRE). JRE provides the files necessary to run Java applications. The Software Development Kit (SDK) provides files necessary for programming Java Applications. (The SDK was once known as the Java Development Toolkit - or JDK)
Q: Which version of Java do I install?
A: Make sure you have the latest Java version (version 6.0 as of 2008).
Q: Why doesn't the ligand appear in the Marvin viewer, it has a name?
A: If the ligand does not have coordinates for all the atoms we do not report its SMILES string.
Q: What is a "biounit"?
A: The biological unit (biounit) is the functional form of the protein. Check out its definintion on the PDBWiki. We provide "corrected" biounit files, where any atoms more than 10 Angstroms from the protein were removed. If a symmetry related molecule was generated and the operation was not applied to the water molecules or ligand, these were rotated in accordance with the symmetry operation.
Q: Help!? I have installed all the required Java components and I'm still having trouble with Eolus Viewer!
A: Email us at BindingMOAD@UMich.edu.