Accessing ER Binding Dataset (Estrogen Receptor)
Blair (2000) and Branham (2002) published the EDKB Estrogen Receptor (ER) binding dataset that was produced expressly as a training set designed for developing predictive models. The data is based on a validated assay using rat uteri. The dataset contains 131 ER binders and 101 non-ER binders. This structurally diverse data set has 312 predictors generated using the Molconn-Z software 4.07 and was analyzed using CERP (Ahn et al., 2007). These training set chemicals were selected for both chemical structure diversity and range of activity, both of which are essential to develop robust QSAR and other models (Perkins, 2003). Guided by the SAR studies described by Fang (2001), the chemicals were selected to provide uniform coverage of a diverse chemical structure domain, as well coverage of an activity range extending down a million-fold below that of the endogenous hormones.
This dataset is available in one of two ways:
Option 1: EDKB Database
Step 1: Run EDKB
Step 2: Select ER binding dataset in "Assay Type" at bottom left panel.
Option 2: Download ER Binding Dataset SD File
You will notice some delay the first time you run EDKB because the entire EDKB application must download the first time you access it. Because future uses of the software will only download any parts of the application that have been changed, the application should start much quicker. You may also be prompted to update your version of Java before EDKB will run.
Possible Error Messages
- "Connection failed: the network adapter could not establish the connection..."
This might be due to your organization's firewall. Many firewalls are set up to only allow traffic to destination port 80 on remote hosts (Web traffic). However, the EDKB server needs to be contacted on port 1528. Thus, you need to contact your system administrator about this particular port number (port 1528) that may need to be opened as an allowed destination port for outgoing connections on your organization's firewall.
The following statement has been prepared for your convenience to communicate with your system administrator:
"The EDKB server edkb.fda.gov is listening on port 1528 for connections from the EDKB client software. An organization whose hosts are to run the EDKB client software needs to allow outgoing connections from any port (source port is randomly chosen on the client as is usual with Internet communications), to the fixed destination port of 1528 on edkb.fda.gov."
- "Couldn't load jnlp file to..."
Follow the steps below to fix the problem:
- Open the "Tools" menu of your Internet browser and select "Internet Options.
- "Select the "General" tab and click the "Settings" button in the "Temporary Internet Files" section.
- Select the "Every visit to the page" radio button.
- Click "OK."
Note: If you still receive the error message after following the steps above, repeat Steps 1 and 2, click the "Delete Files" button instead of the "Settings" button in Step 2 and click OK.
Please address any questions and suggestions to Dr. Weida Tong at 870-543-7142 or firstname.lastname@example.org.